Best Invoicing Software for Agencies (2026)

FreshBooks is one of the most popular invoicing solutions for small agencies and freelancers, known for its user-friendly interface and comprehensive invoicing features. The platform makes it easy to create professional invoices, track time, manage expenses, and accept payments. It's designed for non-accountants, with an intuitive interface that doesn't require accounting knowledge.

The invoicing features are robust, including customizable templates, automatic payment reminders, recurring invoices, and multiple payment methods. FreshBooks integrates time tracking with invoicing, allowing you to bill for tracked hours. The platform includes basic accounting features, expense tracking, and client management. However, FreshBooks is primarily focused on invoicing and basic accounting rather than comprehensive agency management, so agencies needing project management or client portals may need additional tools.

Pricing starts at $17/month for the Lite plan (5 billable clients), with higher tiers at $30/month (50 clients) and $55/month (unlimited clients). Transaction fees are 2.9% + $0.30 for credit cards. The platform offers good value for small agencies, though costs can add up with transaction fees. Setup is straightforward, and FreshBooks provides excellent documentation and support. FreshBooks is ideal for small agencies and freelancers that prioritize easy-to-use invoicing over comprehensive agency management features.

QuickBooks is the industry standard for small business accounting, and its invoicing capabilities are comprehensive. The platform offers robust invoicing features including customizable templates, automatic payment reminders, recurring invoices, and multiple payment methods. However, QuickBooks is primarily an accounting platform with invoicing features, rather than a dedicated invoicing solution.

The platform excels in providing comprehensive accounting features including expense tracking, financial reporting, tax preparation, and payroll. Invoicing integrates seamlessly with accounting, making it easy to track income and expenses. However, QuickBooks is less focused on agency-specific needs like time tracking integration, project management, or client portals. The interface, while powerful, can feel complex for users who just need invoicing. Agencies may need to integrate QuickBooks with other tools for comprehensive agency management.

Pricing starts at $30/month for Simple Start, with higher tiers at $55/month (Essentials) and $85/month (Plus). Transaction fees are 2.9% + $0.25 for credit cards, or 1% for ACH. The platform offers good value for agencies that need comprehensive accounting, though it may be overkill for agencies that just need invoicing. Setup requires some accounting knowledge, and QuickBooks provides extensive documentation and support. QuickBooks is ideal for agencies that prioritize accounting and financial management alongside invoicing.

Harvest excels at time tracking and seamlessly connects time tracking to invoicing, making it ideal for agencies that bill primarily by the hour. The platform makes it easy to track time across projects and clients, then generate invoices directly from tracked hours with customizable rates. This workflow is particularly valuable for agencies with variable billing based on actual time spent.

The invoicing features are solid, including customizable templates, automatic invoice generation from time entries, recurring invoices, and payment processing. Harvest integrates with numerous project management tools, allowing time tracking within existing workflows. However, Harvest is focused on time tracking and invoicing rather than comprehensive agency management, so agencies may need additional tools for CRM, project management, or client portals. The platform is simple and intuitive, making it easy for teams to adopt.

Pricing starts at $12/user/month for unlimited projects, with a free plan available for solo users (1 user, 2 projects). Transaction fees are 2.9% + $0.30 for credit cards. For a 10-person agency, expect $120/month plus transaction fees. The platform offers good value for agencies that prioritize time tracking and time-based billing. Setup is straightforward, and Harvest provides good documentation and support. Harvest is ideal for agencies that bill primarily by the hour and want seamless time-to-invoice workflows.

Bonsai is an all-in-one platform designed specifically for freelancers and small agencies, combining invoicing, contracts, proposals, time tracking, and client management. The platform makes it easy to manage the entire client lifecycle from proposal to payment, with integrated workflows that eliminate manual processes.

The invoicing features are comprehensive, including customizable templates, automatic payment reminders, recurring invoices, and multiple payment methods. Bonsai integrates invoicing with proposals and contracts, creating a seamless workflow. The platform includes time tracking, expense tracking, and basic project management. However, Bonsai is designed for smaller teams and may feel limited for larger agencies. The platform is user-friendly and requires minimal setup, making it ideal for freelancers transitioning to agency work.

Pricing starts at $24/month for the Starter plan, with higher tiers at $39/month (Professional) and $79/month (Business). Transaction fees are 2.9% + $0.30 for credit cards. The platform offers good value for freelancers and small agencies, though larger teams may find it limiting. Setup is straightforward, and Bonsai provides good documentation and support. Bonsai is ideal for freelancers and small agencies (1-5 people) that want comprehensive features without the complexity of enterprise platforms.

Wave offers free invoicing and accounting software, making it attractive for small agencies and freelancers on tight budgets. The platform provides essential invoicing features including customizable templates, automatic payment reminders, recurring invoices, and payment processing. It also includes basic accounting features like expense tracking and financial reporting.

The free tier includes unlimited invoices and clients, making it excellent value for cash-strapped agencies. However, Wave makes money through payment processing fees (2.9% + $0.30 for credit cards, 1% for ACH), which can add up for agencies processing significant volumes. The platform is user-friendly and straightforward, though it lacks advanced features found in paid solutions. Wave is best suited for very small agencies or freelancers just starting out who need basic invoicing without subscription costs.

Pricing is free for invoicing and accounting, with payment processing fees applied only when clients pay. This makes Wave attractive for agencies with low payment volumes, though transaction fees can become expensive for high-volume agencies. Setup is simple, and Wave provides good documentation. Wave is ideal for small agencies and freelancers that prioritize cost savings and need basic invoicing features without subscription fees.

Xero is a cloud-based accounting platform popular among small businesses and agencies, particularly outside the US. The platform offers comprehensive invoicing features including customizable templates, automatic payment reminders, recurring invoices, and multiple payment methods. Xero integrates invoicing seamlessly with accounting, making it easy to track income and expenses.

The platform excels in providing comprehensive accounting features including expense tracking, financial reporting, bank reconciliation, and tax preparation. Xero integrates with numerous third-party tools, providing flexibility for agencies with existing tool stacks. However, Xero is primarily an accounting platform with invoicing features, rather than a dedicated invoicing solution. The interface is modern and user-friendly, though it may feel complex for users who just need invoicing. Agencies may need to integrate Xero with other tools for comprehensive agency management.

Pricing starts at $15/month for the Starter plan (limited invoices), with higher tiers at $42/month (Standard) and $78/month (Premium). Transaction fees vary by payment method. The platform offers good value for agencies that need comprehensive accounting, though it may be overkill for agencies that just need invoicing. Setup requires some accounting knowledge, and Xero provides extensive documentation and support. Xero is ideal for agencies that prioritize cloud-based accounting and financial management alongside invoicing.

PayPal Invoicing provides a simple, free way to create and send invoices, making it attractive for agencies that just need basic invoicing without additional features. The platform integrates seamlessly with PayPal payments, allowing clients to pay invoices directly through PayPal. It's straightforward and requires no subscription fees.

The invoicing features are basic but functional, including customizable templates, automatic payment reminders, and payment tracking. However, PayPal Invoicing is limited compared to dedicated invoicing platforms—it lacks time tracking integration, advanced reporting, expense tracking, or comprehensive client management. The platform is best suited for agencies that need simple invoicing and payment collection without additional business management features. Payment processing fees are standard PayPal rates (2.9% + $0.30 for domestic payments).

Pricing is free for creating invoices, with payment processing fees applied only when clients pay. This makes PayPal Invoicing attractive for agencies with low payment volumes, though transaction fees can become expensive for high-volume agencies. Setup is simple and requires a PayPal account. PayPal Invoicing is ideal for very small agencies or freelancers that need basic invoicing and payment collection without subscription costs or advanced features.