Best Of · Accounting · Agencies

The best accounting software for agencies

Agencies live and die by billable time, project margins, and clean client invoicing. We weighted project and time tracking alongside billing, then ranked the five tools that fit a studio or agency best.

Reviewed by M. HALLORAN·Updated MAY 2026·How we vet
Tools compared 5
Criteria weighted 5
Last reviewed June 2026
Paid placements 0
How we ranked the field

For agencies we weight project tracking, time, and client billing most, since profit hides in the gap between hours worked and hours invoiced. See the full rubric →

Project and time tracking 25%
Client billing 25%
Ease of use 20%
Value for money 15%
Integrations 15%
01
RANK
★ Editor’s Choice

FreshBooks

Best for agencies

Time tracking, projects, and client invoicing are the core of FreshBooks, not bolt ons, which is exactly what an agency needs. Logging hours and turning them into a branded invoice is the smoothest here. Client caps and per user fees are the things to size before you commit.

  • Projects built in
  • Best time to invoice flow
  • Branded client billing
89
OUT OF 100
02
RANK

Xero

Best for teams

Unlimited users suit an agency where account managers, finance, and freelancers all touch the books. The Projects add on tracks time and job profitability, and the reporting is strong. Projects costs extra per user, so factor that into the plan.

88
OUT OF 100
03
RANK

QuickBooks Online

Best for reporting

Projects in the Plus tier track profitability by client, and the reporting answers an owner's margin questions cleanly. The app ecosystem covers almost any agency tool you already run. Time tracking and projects sit higher up the price ladder.

Read the QuickBooks Online verdict → From $38/mo · 50% off 3 mo
87
OUT OF 100
04
RANK

Zoho Books

Best value

Projects, timesheets, and retainer invoicing come built in at a low price, and the wider Zoho suite covers CRM and proposals for an agency. Value is the headline. The interface is busier, and the best fit is teams already leaning on Zoho.

Read the Zoho Books verdict → Free · paid from $20/mo
86
OUT OF 100
05
RANK

Wave

Best free

For a small studio watching costs, free invoicing and accounting cover the essentials, and Pro adds bank imports cheaply. There is no real project or time tracking, so you will pair it with a separate tool as the agency grows.

Read the Wave verdict → Free · Pro $16/mo
80
OUT OF 100

Pricing verified as of June 2026. Vendors change plans often · check the vendor for current pricing.

At a glance

✓ full  ·  ∼ partial  ·  — none
Capability FreshBooksXeroQuickBooks OnlineZoho BooksWave
Project tracking
Built in time tracking
Retainer invoicing
Multiple currencies
Built in payroll
Open API