A note before you read: ABFI doesn't sell software and has no affiliate deals. We work mostly in QuickBooks Online and have tried to be fair to the rest.
Agency owners rarely need fancier accounting software. They need their existing software to answer "which clients and services make money?" That takes three things: a chart of accounts that separates delivery cost from overhead, a way to track time or allocate costs to clients, and someone closing the books monthly. Keep that in mind as you read the list.
What agency accounting software needs to do
| Need | Why |
|---|---|
| Projects or customer-level reporting | Profit by client |
| Classes or tracking categories | Profit by service line (paid media, SEO, creative) |
| Recurring invoices | Retainers |
| Integration with time tracking | Delivery salaries allocated to clients |
| Deferred revenue handling | Retainers billed in advance |
| Multi-currency (if you have overseas clients) | Clean receivables |
The shortlist
1. QuickBooks Online (Plus or Advanced): best for most agencies
- Why: Projects and classes for client and service-line reporting, recurring invoices, and the widest choice of accountants and integrations [1]. Advanced adds more users, roles and custom reporting. See QuickBooks Online Plus vs Advanced and classes vs locations.
- Watch for: deferred revenue for retainers is manual or needs an add-on.
2. Xero: best for agencies with international clients or a Xero accountant
- Why: strong multi-currency on higher plans, tracking categories for service lines, projects, and a clean interface [2].
- Watch for: tracking categories are limited in number, so plan them carefully. Compare: QuickBooks Online vs Xero.
3. FreshBooks: best for solo consultants and very small studios
- Why: built around invoicing, time tracking and getting paid, with a friendly interface [3].
- Watch for: reporting and accounting depth are lighter than QuickBooks or Xero, so growing agencies often move on. See QuickBooks vs FreshBooks.
4. Sage Intacct: best for larger agencies and agency groups
- Why: dimension-based reporting (client, project, department, entity), multi-entity consolidation and stronger controls [4].
- Watch for: implementation cost and time. Usually makes sense for agencies with a finance team or several entities.
Tools that sit next to your accounting software
- Harvest: time tracking and invoicing that connects to QuickBooks and Xero [5]. Popular with agencies that need time data for client profitability.
- Agency management platforms (for example, Productive): combine time tracking, budgets, resourcing and profitability for agencies, and sync with accounting software [6].
These don't replace the general ledger. They feed it the data that makes profit by client possible.
Which setup at which size?
| Your agency | Usual best fit |
|---|---|
| Solo consultant | FreshBooks, or QuickBooks Online Simple Start |
| Small agency, under 10 people | QuickBooks Online Plus or Xero, plus Harvest |
| Growing agency, 10 to 50 people | QuickBooks Online Advanced or Xero, plus an agency management tool |
| Agency group, several entities | Sage Intacct (or similar), with a finance team or outsourced department |
Software is the easy part
The same software gives one agency perfect client margins and another agency a meaningless P&L. The difference is setup: see our chart of accounts for agencies and agency profit by client. Our tech stack guide shows how the tools fit together.
Rather have someone run it? See the best bookkeeping services for agencies. ABFI's agency accounting runs inside QuickBooks Online.
Keep reading
- Chart of accounts for marketing agencies
- QuickBooks vs FreshBooks
- Best bookkeeping services for agencies
Sources
- Intuit, QuickBooks Online plans and pricing, quickbooks.intuit.com/pricing. Checked November 6, 2026.
- Xero, US pricing and features, www.xero.com/us/pricing-plans. Checked November 6, 2026.
- FreshBooks, pricing and features, www.freshbooks.com/pricing. Checked November 6, 2026.
- Sage Intacct, product website, www.sage.com/en-us/sage-business-cloud/intacct. Checked November 6, 2026.
- Harvest, integrations, www.getharvest.com/integrations. Checked November 6, 2026.
- Productive, company website, productive.io. Checked November 6, 2026.
Questions owners ask
What accounting software do most marketing agencies use?
QuickBooks Online and Xero are the most common for small and mid-size agencies, usually with a separate time-tracking tool.
Is FreshBooks good for agencies?
For solo consultants and very small studios, yes. Growing agencies often need the deeper reporting of QuickBooks or Xero.
How do I track profit by client in my accounting software?
Use projects or customers for clients, classes or tracking categories for service lines, and allocate delivery salaries to clients from time-tracking data.
When should an agency move to Sage Intacct?
Usually when you have several entities, a finance team, or reporting needs that QuickBooks or Xero can't meet without heavy spreadsheet work.
Do I need a separate time-tracking tool?
If you want profit by client, almost always. Time data is what lets you assign your biggest cost, people, to each client.
Want client margins you can trust?
ABFI sets up agency books for client profitability and closes them monthly. Start with a complimentary Business Accounting Diagnostic.