Best Accounting Software for Agencies (2026)
We compared 10 leading accounting solutions for agencies. Compare invoicing, expense tracking, financial reporting, tax prep, and multi-currency support.
Agencies need accounting software that handles project-based billing, retainers, and expense tracking while integrating with project management and client workflows. This guide compares tools across invoicing, expense tracking, financial reporting, tax preparation, and multi-currency support to help you choose the right fit.
Quick Comparison
| Tool | Best For | Starting Price | Key Feature | Rating |
|---|---|---|---|---|
1AgencyPro Editor's Pick | All-in-one agency ops | $99/month | Accounting + project management | 4.3/5 |
2QuickBooks | Small business accounting | $30/month | Industry-standard bookkeeping | 4.6/5 |
3Xero | Cloud accounting | $15/month | Beautiful cloud accounting | 4.6/5 |
4FreshBooks | Freelancers & agencies | $19/month | Simple invoicing & time tracking | 4.5/5 |
5Wave | Budget-conscious agencies | Free | Free accounting & invoicing | 4.4/5 |
6Bench | Bookkeeping outsourcing | $249/month | Bookkeepers do the work | 4.5/5 |
7Sage | Mid-size agencies | $34/month | Robust accounting suite | 4.4/5 |
8Zoho Books | Zoho ecosystem users | $15/month | Integrated with Zoho suite | 4.4/5 |
9NetSuite | Enterprise agencies | Custom | ERP for large organizations | 4.3/5 |
10FreeAgent | UK-based agencies | $24/month | UK-focused accounting | 4.5/5 |
Feature Comparison
| Tool | Invoicing | Expense Tracking | Financial Reporting | Tax Prep | Multi-Currency |
|---|---|---|---|---|---|
| AgencyPro | |||||
| QuickBooks | |||||
| Xero | |||||
| FreshBooks | |||||
| Wave | |||||
| Bench | |||||
| Sage | |||||
| Zoho Books | |||||
| NetSuite | |||||
| FreeAgent |
Detailed Reviews
AgencyPro
Best for agencies wanting accounting integrated with project management and client portal
AgencyPro combines invoicing, expense tracking, and financial reporting with project management, time tracking, CRM, and client portals. Bills are generated from logged time and projects, eliminating double entry. Retainer billing is built in with utilization tracking. Clients pay through the white-label portal.
AgencyPro syncs with QuickBooks and Xero for full accounting and tax prep, so you get the best of both: project-centric billing in AgencyPro and GAAP-ready books in your accountant's preferred tool. Pricing starts at $99/month with unlimited users. Best for small to mid-size agencies that want ops and accounting in one place.
Setup is fast, support is responsive, and the platform is designed specifically for agencies. Ideal if you want time tracking, projects, and invoicing tightly integrated without juggling separate systems.
Pros
- • Invoicing tied to projects and time
- • Retainer billing with utilization
- • Syncs to QuickBooks and Xero
- • Client portal and payment processing
Cons
- • Not a full replacement for CPA-led accounting
- • No native multi-currency
QuickBooksVisit website →
Best for Small business accounting
QuickBooks is the industry standard for small business accounting. Strong invoicing, expense tracking, reporting, and tax prep. Integrates with many agency tools. Best when paired with project management for time-to-invoice workflow.
XeroVisit website →
Best for Cloud accounting
Xero offers beautiful cloud accounting with strong bank feeds, multi-currency, and a robust app ecosystem. Popular with agencies who want modern, cloud-native accounting. Good integration options.
FreshBooksVisit website →
Best for Freelancers & agencies
FreshBooks combines simple invoicing with time tracking and expense management. Built for service businesses. Easy to use, good client-facing invoices. Lacks advanced accounting features but sufficient for many agencies.
WaveVisit website →
Best for Budget-conscious agencies
Wave provides free invoicing, expense tracking, and basic reporting. Revenue comes from payment processing. Good for very small agencies and freelancers. Limited integrations and support.
BenchVisit website →
Best for Bookkeeping outsourcing
Bench pairs software with real bookkeepers who categorize transactions and produce financials. Ideal for agencies that want done-for-you bookkeeping. Premium pricing but saves significant time.
SageVisit website →
Best for Mid-size agencies
Sage offers a robust accounting suite with strong reporting and compliance features. Good for agencies outgrowing QuickBooks. More complex setup and steeper learning curve.
Zoho BooksVisit website →
Best for Zoho ecosystem users
Zoho Books integrates seamlessly with Zoho CRM, Projects, and other Zoho apps. Affordable and capable. Best if you already use Zoho for other functions.
NetSuiteVisit website →
Best for Enterprise agencies
NetSuite is a full ERP for large organizations. Handles complex revenue recognition, multi-entity, and global operations. Overkill for most agencies; consider only at significant scale.
FreeAgentVisit website →
Best for UK-based agencies
FreeAgent is built for UK freelancers and small businesses with UK tax and VAT handling. Good for UK-based agencies. Less relevant for US-focused shops.
How We Evaluated These Tools
Our evaluation process considered multiple factors critical to agency accounting software:
- Agency Chart of Accounts: Does the software support agency-specific account structures like retainer revenue, project costs, and contractor payments? A tailored chart of accounts simplifies reporting.
- Project Profitability Tracking: Can you track revenue and costs at the project level? Understanding per-project margins is critical for pricing and resource decisions.
- Multi-Currency Support: Does the tool handle invoicing and reporting in multiple currencies? Essential for agencies with international clients or remote contractors.
- Bank Feed Integration: Does the tool sync with bank accounts for automatic transaction import? Bank feeds eliminate manual data entry and speed reconciliation.
- Tax Preparation Features: Does the software support tax categories, year-end reports, and CPA exports? Proper tax prep saves agencies thousands and reduces compliance risk.
- Expense Categorization: Can you categorize expenses by project, client, and type automatically? Granular expense tracking supports accurate profitability analysis.
- Invoicing Capabilities: Does the tool support retainer billing, time-based invoicing, and online payments? Flexible invoicing reduces friction in the client payment cycle.
- Financial Reporting Depth: Does the platform offer P&L, cash flow, balance sheet, and custom reports? Deep reporting powers informed business decisions and forecasting.
We also considered real user reviews, case studies, and industry reputation. Tools were weighted more heavily when they demonstrated strong adoption among agencies specifically, not just general small businesses.
How to Choose Accounting Software for Your Agency
- Invoicing: Support for project-based, retainer, and time-and-materials billing. Client-facing invoices and online payments matter.
- Expense Tracking: Receipt capture, categorization, and project allocation. Integration with corporate cards helps.
- Financial Reporting: P&L, cash flow, project profitability. Ensure reports match how you manage the business.
- Tax Prep: Export to accountants, support for your jurisdiction. Some tools include tax features; others integrate with CPAs.
- Multi-Currency: Essential for international clients. Check exchange rate handling and reporting.
Consider integration with project management and time tracking. All-in-one platforms like AgencyPro reduce data entry by connecting time and projects directly to invoicing.
Frequently Asked Questions
What is the best accounting software for agencies?
The best accounting software for agencies depends on your size and needs. AgencyPro combines accounting with project management, CRM, and client portals for all-in-one ops. QuickBooks and Xero lead for dedicated accounting with strong tax and reporting. FreshBooks suits freelancers and small agencies needing simple invoicing. Wave offers free core features. Bench provides outsourced bookkeeping. For enterprise agencies, NetSuite delivers full ERP capabilities.
Should agencies use dedicated accounting software or all-in-one platforms?
All-in-one platforms like AgencyPro integrate invoicing, time tracking, and expenses with projects and clients—reducing double entry and keeping finances in context. Dedicated accounting tools (QuickBooks, Xero) offer deeper bookkeeping, tax prep, and GAAP compliance. Many agencies use both: AgencyPro (or similar) for project billing and client-facing invoicing, syncing to QuickBooks or Xero for full accounting. This split works when project management drives revenue recognition.
How much does accounting software cost for agencies?
Costs vary: Wave is free (revenue from payment processing). FreshBooks starts at $19/month, Xero at $15/month, QuickBooks at $30/month. AgencyPro is $99/month including accounting features. Bench (bookkeeping) runs $249+/month. NetSuite is enterprise-priced. Add payment processing fees (2.9% + $0.30 typically). Consider total cost: software + transactions + any bookkeeper or CPA time.
What accounting features do agencies need most?
Essential features: invoicing with retainer and time-based billing, expense tracking (receipt capture), financial reporting (P&L, cash flow, project profitability), integration with project management and time tracking, multi-currency if you have international clients, tax prep support or export to accountants. Agencies also benefit from client portal integration so clients can view invoices and pay online.
Can accounting software integrate with agency management tools?
Yes. Most accounting tools integrate with project management, time tracking, and CRMs via native integrations, Zapier, or APIs. AgencyPro syncs with QuickBooks and Xero. FreshBooks has built-in time tracking. Evaluate your workflow: if time drives billing, ensure seamless time-to-invoice flow. Many agencies use AgencyPro for ops and sync to QuickBooks/Xero for full accounting and tax prep.
How do agencies handle retainer billing in accounting software?
Retainer billing requires recurring invoices, utilization tracking, and sometimes draw-down against prepaid amounts. AgencyPro, FreshBooks, and QuickBooks support recurring invoices. AgencyPro adds retainer-specific workflows (usage tracking, surplus/shortfall). QuickBooks can handle retainer revenue recognition with proper setup. Ensure your tool supports your retainer structure—fixed monthly vs. draw-down.
What's the difference between bookkeeping and accounting software?
Bookkeeping is day-to-day record-keeping: invoices, expenses, bank reconciliation. Accounting software (QuickBooks, Xero) handles this. Accounting adds analysis, financial statements, tax preparation, and audit support. Many agencies do bookkeeping in software and hire a CPA for year-end accounting and tax. Bench and similar services provide bookkeepers who use the software—you get done-for-you bookkeeping.
Is Wave accounting software good for agencies?
Wave is a solid free option for small agencies. It offers invoicing, expense tracking, and basic reporting. Limitations: no native project management, limited integrations, no multi-currency on free tier, and support is community-focused. It works for freelancers and very small agencies on a tight budget. As you scale, consider FreshBooks, Xero, or AgencyPro for better project integration and support.
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