Top 10 Billing & Invoicing Software: Features, Pros, Cons & Comparison

Introduction

Billing and invoicing software are specialized digital tools designed to automate the process of creating, sending, and managing financial requests for payment. Unlike broader accounting systems, these tools focus specifically on the transaction layer between a business and its clients. They allow users to generate professional documents, track whether a client has opened an invoice, and provide secure gateways for customers to pay via credit card, bank transfer, or digital wallets.

Modern billing software is crucial because it professionalizes the brand image of a business while significantly reducing the “time-to-payment.” By moving away from manual Word or Excel templates, businesses can avoid calculation errors and missing tax details. Furthermore, these platforms provide essential automation for recurring billing models, such as subscriptions or retainer-based services, ensuring that invoices are sent out on time every month without any manual effort from the business owner.

Real-World Use Cases

1. Subscription Management: A SaaS startup uses billing software to automatically charge thousands of customers’ credit cards on the first of every month and send out digital receipts instantly.
2. Professional Services: A graphic designer sends an invoice to a client that includes a breakdown of hours worked; the client clicks a “Pay Now” button in the email and pays immediately via Apple Pay.
3. Field Services: A plumbing company uses a mobile invoicing app to generate a bill on-site after a repair; the customer signs the digital screen and pays before the technician even leaves the house.
4. Tiered Pricing: A cloud storage provider uses billing software to automatically adjust a customer’s monthly bill based on how many gigabytes of data they used during the previous cycle.
5. Multi-Currency Trade: An e-commerce wholesaler sends an invoice to an international buyer in Euros; the software automatically calculates the exchange rate and tax requirements for that specific region.

Evaluation Criteria for Buyers

• Invoice Customization: How much control do you have over the look and feel of the invoice? Can you add your logo, brand colors, and custom terms?
• Automation Features: Does the software support recurring billing, automated late payment reminders, and auto-scheduling?
• Payment Gateway Support: Which payment processors (Stripe, PayPal, Square) does the tool integrate with, and what are the associated transaction fees?
• Mobile Functionality: Is there a high-quality mobile app for creating and sending invoices on the go?
• Client Portal: Does the software provide a dedicated space where customers can log in to see their full payment history and download past invoices?
• Tax and Compliance: Does the tool automatically calculate sales tax, VAT, or GST based on the customer’s location?
• Reporting and Analytics: Does it provide a clear dashboard showing your total revenue, outstanding balances, and “Average Days to Pay” metrics?

Best for: Freelancers, small business owners, agencies, and subscription-based companies looking to professionalize their billing and speed up collections.

Not ideal for: Large-scale retail operations that require a heavy point-of-sale (POS) hardware presence or companies with extremely complex manufacturing resource planning (MRP) needs.

Key Trends in Billing & Invoicing Software

• Embedded “Click-to-Pay”: Moving from static PDF invoices to interactive web-based invoices with integrated payment buttons.
• Usage-Based Billing: Software that automatically calculates bills based on real-time consumption data (e.g., API calls, storage used).
• AI-Driven Follow-ups: Using machine learning to determine the optimal time to send a reminder to a specific client to maximize payment probability.
• Mobile-First Invoicing: The ability to run an entire billing department from a smartphone, including document generation and signature capture.
• Global E-Invoicing Compliance: Automatic integration with government-mandated digital invoicing portals (like Peppol) across Europe and Asia.
• Personalized Payment Links: Generating unique, secure URLs that can be sent via WhatsApp or SMS for instant mobile payment.
• Cryptocurrency Support: An increasing number of platforms are adding the ability for businesses to accept and settle invoices in stablecoins or Bitcoin.
• Automated Dispute Resolution: Built-in communication channels where clients can flag a specific line item for discussion without delaying the entire payment.
• Real-Time Cash Flow Forecasting: Visual tools that project future bank balances based on the “due dates” of current outstanding invoices.
• Open Banking Integration: Direct “account-to-account” payments that bypass traditional card networks to reduce transaction fees.

How We Selected These Tools (Methodology)

The selection of these top billing and invoicing tools is based on an analysis of the current financial technology market:

• Evaluation of the platform’s invoice design engine and professional template variety.
• Assessment of the automation capabilities for recurring revenue and dunning (reminder) sequences.
• Review of the integration depth with major payment gateways and third-party apps.
• Analysis of the user experience on both desktop and mobile platforms for both the business and the client.
• Consideration of the price-to-feature ratio, specifically for growing small businesses.
• Verification of the platform’s ability to handle international tax and multi-currency requirements.
• Assessment of the vendor’s reliability and historical uptime for payment processing.

Top 10 Billing & Invoicing Software

1.FreshBooks

FreshBooks is a leading platform designed specifically for service-based small businesses and freelancers who need an intuitive, all-in-one billing solution.

Key Features

• Professional Invoice Creator: Highly customizable templates that can be generated in seconds.
• Retainer Billing: Specialized tools for managing clients who pay a set fee upfront every month.
• Automated Late Fees: Automatically add a percentage or flat fee to invoices that pass their due date.
• Time Tracking: Integrated timer that allows you to turn billable hours directly into an invoice.
• Client Command Center: A portal where clients can view, print, and pay all their outstanding bills.
• Expense Management: Snap photos of receipts and automatically categorize them for tax season.

Pros

• Widely considered the most user-friendly interface in the invoicing software market.
• Exceptional customer support and a very strong mobile app experience.

Cons

• The “Lite” plan has a strict limit on the number of billable clients you can have.
• Does not offer the deep inventory management features needed for large e-commerce businesses.

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• SOC 2 Type II, PCI DSS
• GDPR

Integrations & Ecosystem

Broad support for the most popular productivity and payment tools.

• Stripe
• PayPal
• G Suite
• Slack

Support & Community

Excellent live phone support and a massive library of educational webinars for entrepreneurs.

2.Zoho Invoice

Zoho Invoice is a powerful, feature-rich invoicing tool that is uniquely offered as a completely free solution for small businesses.

Key Features

• Complete Customization: High level of control over the layout and data fields of every invoice.
• Customer Portal: Dedicated space for clients to manage their own payments and estimates.
• Recurring Invoices: Automated scheduling for long-term projects or subscriptions.
• Workflow Automation: Set up custom triggers, such as sending a “Thank You” email once a payment is received.
• Multi-Currency Support: Handles payments in over 10 countries and localized languages.
• Timesheet Billing: Easily convert tracked project time into professional invoices.

Pros

• Unbeatable value, as the core invoicing features are free for businesses under a certain revenue threshold.
• Seamlessly integrates with the massive Zoho ecosystem of CRM and workplace tools.

Cons

• The interface can feel slightly cluttered due to the high number of configuration options.
• Advanced users might find the reporting to be less “polished” than some premium competitors.

Platforms / Deployment

• Web / iOS / Android / Windows
• Cloud

Security & Compliance

• SOC 2, ISO 27001
• GDPR, HIPAA

Integrations & Ecosystem

Deeply connected to the Zoho suite and several major third-party processors.

• Zoho CRM
• Stripe
• Square
• PayPal

Support & Community

Robust community forums and a very responsive email support team.

3.Invoice2go

Invoice2go is a mobile-first invoicing solution built for small businesses and contractors who spend more time in the field than at a desk.

Key Features

• Simple Mobile Creator: Optimized for fast invoice generation on a smartphone screen.
• Estimates and Quotes: Convert professional quotes into invoices with a single tap once the client approves.
• Instant Payment Notifications: Get a push notification the moment a client views or pays an invoice.
• Business Reporting: Simple charts showing your sales, taxes, and aging reports.
• Reviews Integration: Automatically ask customers for a Google or Facebook review after they pay.
• Map Integration: Track where your jobs are located and manage your service area.

Pros

• Perfect for “on-the-job” professionals like landscapers, photographers, or electricians.
• Extremely fast learning curve; you can send your first invoice within minutes of downloading.

Cons

• Lacks the advanced accounting and ledger features of a full-scale financial tool.
• Customization of templates is more limited compared to desktop-focused platforms.

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• PCI DSS
• GDPR

Integrations & Ecosystem

Focuses on connecting with essential payment and communication apps.

• QuickBooks
• Xero
• Stripe
• PayPal

Support & Community

Help center focused on “how-to” guides for mobile-centric business owners.

4.Wave Invoicing

Wave is a popular choice for micro-businesses and solopreneurs who want a professional invoicing tool without a monthly subscription fee.

Key Features

• Unlimited Invoices: No caps on the number of invoices or clients, even on the free version.
• Recurring Billing: Automated credit card processing for long-term clients.
• Professional Templates: A selection of modern, clean layouts that look great on any device.
• Integrated Payments: Accept credit cards and bank transfers directly (standard transaction fees apply).
• Automatic Sync: Invoices automatically update your Wave Accounting records for easy bookkeeping.
• Customer Statement: Generate a full summary of a client’s transaction history for a specific period.

Pros

• Completely free to use for invoicing, which is a massive benefit for startups with low overhead.
• One of the cleanest and most minimalist designs in the industry.

Cons

• The customer support for free users is primarily limited to self-service help articles.
• Not intended for medium or large businesses that require complex multi-user permissions.

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• PCI DSS Level 1
• GDPR

Integrations & Ecosystem

Well-connected to the broader Wave ecosystem and major North American banks.

• Wave Accounting
• Wave Payroll
• Google Sheets
• Zapier

Support & Community

Large active community and a helpful automated chat assistant for common queries.

5.Square Invoices

Square Invoices is a robust tool that bridges the gap between digital billing and physical point-of-sale transactions.

Key Features

• Instant Deposits: Get access to your funds as soon as the client pays the invoice.
• Progress Billing: Create a schedule of payments for large projects (e.g., 25% upfront, 75% on completion).
• Milestone Tracking: Associate specific payments with project phases or delivery dates.
• On-the-spot Payments: Accept a card in person to close an open invoice using Square hardware.
• Automatic Reminders: Smart reminders that escalate in tone as an invoice becomes more overdue.
• Contract Integration: Attach legally binding contracts or terms of service directly to the invoice.

Pros

• Unrivaled for businesses that do a mix of in-person and remote service work.
• The “Instant Deposit” feature is a major advantage for businesses with tight cash flow.

Cons

• Processing fees can be higher than competitors if you aren’t using the full Square ecosystem.
• The customization of the actual invoice document is more “utilitarian” and less “artistic.”

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• PCI DSS Level 1
• GDPR

Integrations & Ecosystem

Directly connected to the massive Square suite of business and retail software.

• Square POS
• Square Appointments
• Wix
• WooCommerce

Support & Community

Excellent phone and email support with a focus on retail and service industry expertise.

6.Invoice Ninja

Invoice Ninja is a leading open-source invoicing platform that offers extreme customization and transparency for tech-savvy business owners.

Key Features

• Custom URL: Host your invoicing portal on your own domain (e.g., https://www.google.com/search?q=billing.yourbrand.com).
• Live PDF Generation: See a real-time preview of the invoice as you type in the details.
• Kanban Boards: Track the progress of projects and convert them into bills in one workspace.
• Task & Time Tracking: Integrated tools to manage your daily workflow and bill for it.
• Buy Now Buttons: Embed payment links directly into your website or emails.
• Inventory Management: Track stock levels and automatically update them when an invoice is sent.

Pros

• Offers a level of control and white-labeling that most “closed” SaaS platforms cannot match.
• The “Pro” plan is exceptionally affordable and packed with features.

Cons

• The interface can be overwhelming for non-technical users who just want a “simple” button.
• Setting up the self-hosted version requires server management knowledge.

Platforms / Deployment

• Web / iOS / Android / Desktop
• Cloud / Self-Hosted

Security & Compliance

• PCI DSS
• GDPR

Integrations & Ecosystem

Supports an incredible range of over 40 different payment gateways globally.

• Stripe
• PayPal
• Authorize.net
• Braintree

Support & Community

Vibrant open-source community and very detailed technical documentation.

7.Chargebee

Chargebee is an enterprise-grade billing platform that specializes in the complexities of subscription revenue and recurring billing cycles.

Key Features

• Flexible Billing Logic: Manage trials, coupons, add-ons, and “freemium” models effortlessly.
• Revenue Recognition: Automated accounting that ensures compliance with global financial standards.
• Dunning Management: Advanced strategies for recovering failed credit card payments.
• Global Tax Engine: Handles VAT, GST, and Sales Tax for customers in over 100 countries.
• Self-Service Billing Portal: Advanced customer portal where users can upgrade or downgrade their own plans.
• Churn Analytics: Deep insights into why customers are leaving and how it affects your MRR.

Pros

• The Gold Standard for SaaS companies that have complex, fast-growing subscription models.
• Automates the “nightmare” of global tax compliance for digital products.

Cons

• The pricing is significantly higher than simple invoicing tools and is based on your revenue.
• It is a “heavy” tool that requires a dedicated person or team to manage and configure.

Platforms / Deployment

• Web
• Cloud

Security & Compliance

• SOC 1, SOC 2, PCI DSS Level 1
• GDPR, HIPAA

Integrations & Ecosystem

Designed to be the “billing engine” that sits between your website and your accounting software.

• Salesforce
• NetSuite
• Stripe
• HubSpot

Support & Community

Enterprise-level account management and a focus on high-growth scaling expertise.

8.Stripe Invoicing

Stripe Invoicing is a high-performance, developer-friendly tool that allows businesses to get paid faster using Stripe’s world-class payment rails.

Key Features

• Hosted Invoice Page: A secure, mobile-optimized web page where clients can pay instantly.
• Smart Retries: Uses machine learning to retry failed payments at the time most likely to succeed.
• One-Click Payments: Customers can use saved cards (Link) to pay an invoice in seconds.
• Line Item Taxing: Automatically apply the correct tax rates for every individual item on the bill.
• Post-Payment Actions: Automatically trigger webhooks or emails once a payment is confirmed.
• Financial Reports: Integrated reporting on revenue, taxes, and net income within the Stripe Dashboard.

Pros

• If you are already using Stripe for your payments, this is the most seamless way to add invoicing.
• The conversion rates for their hosted invoice pages are among the highest in the industry.

Cons

• Lacks the “business management” features like time-tracking or project management found in FreshBooks.
• The pricing is based on a percentage of the invoice volume, which can be expensive for large bills.

Platforms / Deployment

• Web / Mobile App
• Cloud

Security & Compliance

• PCI DSS Level 1
• GDPR

Integrations & Ecosystem

The core of the Stripe platform, connecting to thousands of other apps via API.

• Shopify
• Intercom
• Slack
• Zapier

Support & Community

Excellent technical documentation and a massive global network of developers.

9.Scoro

Scoro is a comprehensive work management solution that treats invoicing as the final step in a unified project management workflow.

Key Features

• End-to-End Workflow: Manage quotes, projects, time-tracking, and billing in one single tool.
• Automated Late Reminders: Set up rules-based follow-ups that look personalized.
• Dynamic Invoicing: Automatically pull data from project timesheets or external apps.
• Multi-Entity Billing: Manage different brands or legal entities within a single account.
• Financial KPI Dashboards: Track your profitability and margins in real-time.
• Margin Tracking: See exactly how much profit you are making on every individual invoice.

Pros

• Exceptional for agencies or consultancies that want one tool to run their entire business operation.
• Eliminates the need for “bridge” apps to move data from project management to billing.

Cons

• The high feature density means it has a steeper learning curve than dedicated invoicing apps.
• The price per user is high, making it a significant investment for a small team.

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• SOC 2 Type II
• GDPR

Integrations & Ecosystem

Focuses on high-quality integrations with major enterprise software suites.

• Microsoft Dynamics
• SAP
• Google Drive
• QuickBooks Online

Support & Community

Personalized onboarding and a focus on operational efficiency for professional services.

10.QuickBooks Invoicing

QuickBooks provides a standard-setting invoicing tool that is part of the world’s most popular accounting ecosystem for small businesses.

Key Features

• Automated Matching: Invoices are automatically matched with incoming bank transactions.
• Custom Branding: Professional templates that can be adjusted to match your company’s identity.
• Progress Invoicing: Bill customers as you complete different phases of a job.
• Instant “Pay Now” Links: Send a link via any messaging app for immediate payment.
• Tax Readiness: Every invoice is automatically categorized for your year-end tax returns.
• Audit Trail: Track when the invoice was sent, viewed, and paid by the customer.

Pros

• The gold standard for financial reliability; your accountant will likely already know how to use it.
• Provides a seamless path from a single invoice to a full balance sheet and P&L report.

Cons

• The software can feel “heavy” if you only need a simple way to send two or three bills a month.
• Monthly subscription costs have been rising steadily over the past several cycles.

Platforms / Deployment

• Web / iOS / Android
• Cloud

Security & Compliance

• SOC 2 Type II, PCI DSS
• GDPR

Integrations & Ecosystem

The largest ecosystem in the world for small business financial software.

• Shopify
• Amazon
• PayPal
• TSheets

Support & Community

Massive network of “ProAdvisors” and accountants who can help you set up and manage the software.

Comparison Table

Tool Name	Best For	Platform(s) Supported	Deployment	Standout Feature	Public Rating
FreshBooks	Service Businesses	Web, iOS, Android	Cloud	Retainer Billing	4.5/5
Zoho Invoice	Micro-Business / Free	Web, iOS, Android	Cloud	100% Free Version	4.6/5
Invoice2go	Field Contractors	Web, iOS, Android	Cloud	Mobile-First UX	4.4/5
Wave	Solopreneurs	Web, iOS, Android	Cloud	Simple & Free	4.4/5
Square	Hybrid Retail/Service	Web, iOS, Android	Cloud	Instant Deposits	4.7/5
Invoice Ninja	Customization	Web, iOS, Android	Self-Host/Cloud	White-labeling	4.8/5
Chargebee	SaaS Subscriptions	Web	Cloud	Complex Dunning	4.6/5
Stripe	Developers / Speed	Web, Mobile	Cloud	Machine Learning Retries	4.7/5
Scoro	Agency Workflow	Web, iOS, Android	Cloud	Integrated Profitability	4.5/5
QuickBooks	Complete Accounting	Web, iOS, Android	Cloud	Accountant Sync	4.3/5

Evaluation & Scoring of Billing & Invoicing Software

Tool Name	Core (25%)	Ease (15%)	Integrations (15%)	Security (10%)	Performance (10%)	Support (10%)	Value (15%)	Weighted Total
FreshBooks	9	10	9	9	9	10	8	9.10
Zoho Invoice	8	9	9	9	9	8	10	8.85
Invoice2go	8	10	8	9	9	8	8	8.45
Wave	8	9	8	9	8	7	10	8.30
Square	9	9	9	10	10	9	9	9.25
Invoice Ninja	10	7	10	9	9	8	10	9.05
Chargebee	10	7	10	10	10	9	7	8.85
Stripe	9	9	10	10	10	8	8	9.05
Scoro	10	7	9	9	9	9	7	8.55
QuickBooks	9	8	10	9	9	8	8	8.60

How to Interpret These Scores

• Weighted Totals: A score above 9.0 represents a platform that is a market leader in its category, balancing professional features with reliable financial performance.
• Ease vs. Power: Tools like Invoice2go and FreshBooks lead in “Ease of Use,” while Chargebee and Scoro lead in “Core Features” for complex business structures.
• Value Metric: This reflects the functionality provided relative to the subscription cost, with free tools like Zoho and Wave naturally scoring high in this category.

Which Billing & Invoicing Software Is Right for You?

Solo / Freelancer

Freelancers need a tool that looks professional but doesn’t take much time to manage. You want to spend your time on your work, not on your billing software.

• Recommendation: FreshBooks or Wave.
• Why: FreshBooks offers the best experience for service providers, while Wave is the best option for those who want a powerful tool at zero monthly cost.

Small Agency / Consultancy

Agencies need to track time, manage multiple clients, and often bill for specific project milestones.

• Recommendation: Scoro or Invoice Ninja.
• Why: Scoro manages your entire workflow, while Invoice Ninja allows you to white-label the portal so your branding is the only thing the client sees.

Field Service (Contractors/Trades)

If you are on the road all day, you need a tool that works flawlessly on a phone and can accept payments the moment the job is done.

• Recommendation: Square Invoices or Invoice2go.
• Why: These tools are optimized for mobile speed and integrated with payment hardware, ensuring you don’t have to “chase” clients for payment later.

SaaS / Subscription Startup

If your business relies on recurring revenue, you need a tool that manages “dunning” (failed payments) and global tax compliance automatically.

• Recommendation: Chargebee or Stripe Invoicing.
• Why: These platforms are the foundation of the modern subscription economy and are designed to handle millions of automated transactions.

Budget vs Premium

If you are just starting out, Zoho Invoice or Wave provide professional results for free. As you grow, moving to a premium tool like QuickBooks or FreshBooks is worth the investment for the time-saving automations and advanced reporting.

Feature Depth vs Ease of Use

If you are non-technical, avoid tools like Invoice Ninja or Chargebee, which have steep learning curves. Stick with FreshBooks or Square, where the interface is designed to guide you through the process step-by-step.

Integrations & Scalability

Always choose a tool that integrates with the payment processor you already use. If you plan to grow from 5 clients to 500, ensure the platform you choose doesn’t have “per-client” pricing that will become unaffordable as you succeed.

Frequently Asked Questions

What is the difference between invoicing and accounting software?

Invoicing software is used to request money from clients (AR), while accounting software tracks your entire financial health, including expenses, payroll, and taxes (the General Ledger).

How much do these tools cost?

Many offer free tiers for small volumes. Paid tiers typically range from $15 to $50 per month. Additionally, you will pay transaction fees (usually around 2.9% + $0.30) to the payment processor.

Can I send invoices in different currencies?

Yes, most modern tools allow you to select the currency for each client. Some, like Chargebee and Stripe, will also automatically handle the tax calculations for those regions.

Is it safe for my customers to pay through these portals?

Yes. These platforms use bank-level encryption (PCI DSS compliance) to ensure that credit card data is never stored on your servers and is handled securely by the payment gateway.

Can I automate my late payment reminders?

Almost all the tools on this list allow you to set a schedule (e.g., 3 days before due, on the due date, and 7 days after) so you never have to manually ask for money.

What is a “Client Portal”?

It is a private website where your client can log in to see every invoice you’ve ever sent them, pay open bills, and download receipts for their own tax records.

Can I use my own logo on the invoices?

Yes, every professional tool on this list allows you to add your logo. Some premium versions also allow you to remove the software’s branding (“Powered by…”) entirely.

How does “Progress Billing” work?

It allows you to split a single large project into several smaller invoices based on a percentage or a set dollar amount as project milestones are reached.

Can I track time within these apps?

Yes, FreshBooks, Scoro, and Zoho Invoice have built-in timers that allow you to track work and instantly convert those hours into a billable invoice.

Do I need a special bank account to accept digital payments?

No, you can usually link your existing business or personal bank account to the payment processor (like Stripe or PayPal) integrated into the invoicing software.

Conclusion

The right billing and invoicing software acts as a silent partner that ensures your business stays liquid and professional. By choosing a platform that fits your specific business model—whether it’s the mobile-friendly Square for field work or the subscription-optimized Chargebee—you can stop worrying about “getting paid” and start focusing on “doing the work.” We recommend setting up your brand colors and a professional “thank you” template immediately to ensure every client interaction feels consistent and high-end.