Best Accounting Software for Agencies
The 5 accounting software we recommend if you're running a team that delivers services to multiple clients — independently scored on the same five-criterion rubric, filtered to the picks that actually fit how you work.
Short answer
The best accounting software for agencies and small teams are Gusto, Deel, Xero. Gusto is our top pick at 9/10. If budget is tight, Deel has the best free plan.
Our top picks for agencies
Gusto
9/10
Highest-scoring pick at 9/10 — best for US-based agencies and studios with a mix of W-2 employees and 1099 contractors.
- ✓Automated payroll tax filings — federal, state, and local handled automatically
- ✓1099 contractor payments and management alongside employee payroll
Deel
9/10
Strongest capability-per-dollar — value score 8/10.
- ✓Hire legally in 150+ countries without setting up a local entity
- ✓Contractor management (contracts, invoicing, payments) free for up to 200 contractors
FreshBooks
8.2/10
Smoothest setup — ease-of-use score 9/10.
- ✓Extremely easy to use
- ✓Beautiful invoices
All 5 accounting software for agencies, ranked
Gusto
Top pickPayroll, benefits, and HR for small businesses
Gusto is the leading payroll and HR platform for US small businesses, handling full-service payroll (direct deposit, tax filings, W-2s, and 1099s), employee benefits (health insurance, 401k), and basic HR tools (offer letters, onboarding checklists, PTO tracking). It automates federal, state, and local payroll tax filings — one of the most time-consuming compliance tasks for small business owners. Gusto is contractor-friendly, making it popular with agencies and studios that mix employees and freelancers.
Strengths
- ✓Automated payroll tax filings — federal, state, and local handled automatically
- ✓1099 contractor payments and management alongside employee payroll
- ✓Employee benefits (health, dental, 401k) integrated in one system
Watch-outs
- ✗US-only — not suitable for international payroll (use Deel)
- ✗Per-person pricing adds up as headcount grows
- ✗No free plan
Deel
Hire and pay contractors and employees in 150+ countries
Deel solves international hiring compliance — it lets businesses hire full-time employees and contractors in 150+ countries without setting up a local legal entity. Deel acts as the Employer of Record (EoR), handling local employment contracts, tax compliance, and payroll in each country. For contractors, Deel manages contracts, invoicing, and payments in local currencies. Built for globally distributed teams. Critical infrastructure for agencies and remote-first businesses hiring internationally.
Strengths
- ✓Hire legally in 150+ countries without setting up a local entity
- ✓Contractor management (contracts, invoicing, payments) free for up to 200 contractors
- ✓Handles local tax compliance, social contributions, and mandatory benefits automatically
Watch-outs
- ✗Employer of Record service carries a significant per-employee monthly fee
- ✗Not the right tool for US-only hiring (Gusto is simpler and cheaper)
- ✗EoR margins vary by country — can be expensive in some markets
Xero
Beautiful accounting software for small businesses
Xero is a cloud-based accounting platform popular outside the US, particularly in the UK, Australia, and New Zealand. It's cleaner and more modern than QuickBooks, with excellent multi-currency support and a strong app marketplace.
Strengths
- ✓Best multi-currency accounting
- ✓Cleaner UI than QuickBooks
- ✓Strong international accounting standards support
Watch-outs
- ✗Less popular with US accountants than QuickBooks
- ✗Starter plan has invoice/bill limits
- ✗Payroll only available in select countries
FreshBooks
Invoicing and accounting for small businesses
FreshBooks is an accounting and invoicing platform designed for service businesses and freelancers. It covers invoicing, expense tracking, time tracking, estimates, and basic double-entry accounting. Much easier to use than QuickBooks, though less powerful for complex accounting needs.
Strengths
- ✓Extremely easy to use
- ✓Beautiful invoices
- ✓Time tracking built in
Watch-outs
- ✗Client limit on lower plans
- ✗Less powerful than QuickBooks for complex accounting
- ✗No payroll
QuickBooks
Small business accounting that does the heavy lifting
QuickBooks is the dominant small business accounting software in the US. It handles invoicing, expense tracking, payroll, tax preparation, and financial reporting. Best for businesses that work with a bookkeeper or accountant.
Strengths
- ✓Gold standard for accountants and bookkeepers
- ✓Comprehensive payroll features
- ✓Huge integration ecosystem
Watch-outs
- ✗Steeper learning curve than FreshBooks
- ✗Pricing increases significantly on higher tiers
- ✗Can be overkill for solo freelancers
Accounting Software for agencies, compared
| Tool | Score | From | Free plan | Ease | Value | Get it |
|---|---|---|---|---|---|---|
| Gusto | 9/10 | — | No | 8.5/10 | 8.5/10 | Review → |
| Deel | 9/10 | — | Yes | 8/10 | 8/10 | Review → |
| Xero | 8.3/10 | $15/mo | No | 8/10 | 8/10 | Try → |
| FreshBooks | 8.2/10 | $19/mo | No | 9/10 | 7.5/10 | Try → |
| QuickBooks | 8/10 | $17/mo | No | 7/10 | 7.5/10 | Try → |
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Frequently asked questions
What is the best accounting software for agencies?
Gusto is our top pick at 9/10 — the strongest fit if you're running a team that delivers services to multiple clients.
What's the best free accounting software for agencies?
Deel offers the best free plan in this list — a genuine way to get going at $0.