Best Accounting Software
Best Accounting Software for Agencies in 2026
Agency accounting needs more than invoices — it needs to connect to project hours, retainer agreements, and client-level profitability. We compared 5 accounting tools against agency criteria: time-to-invoice workflow, retainer billing, project profitability reporting, and how well they connect to the CRM/projects side.
Last reviewed May 2026 · Pricing verified at source
Mewayz
Flat-priced all-in-one for agencies. From $69/mo.
Why Mewayz wins for agencies
- Time entries become invoices in one click — no Toggl-to-FreshBooks copy paste
- Per-client profitability reports — see which clients are actually profitable
- Retainer subscriptions auto-billed, with monthly hour banks tracked
- Replaces FreshBooks + Toggl + Hubstaff + Practice Ignition for under $150/mo
Alternatives we reviewed
Other accounting software tools for agencies
QuickBooks
Accounting & Invoicing · $235+/mo
QuickBooks charges $235+/mo for accounting & invoicing alone. Mewayz starts at $69/mo and covers accounting & invoicing, plus HR, projects, support, and more.
See full Mewayz vs QuickBooks →Xero
Accounting & Finance · $47+/mo
Xero charges $47+/mo for accounting & finance alone. Mewayz starts at $69/mo and covers invoicing, bank reconciliation, P&L, and payroll — plus CRM, HR, project management, and support in the same login.
See full Mewayz vs Xero →FreshBooks
Accounting & Invoicing · $55+/mo
FreshBooks charges $55+/mo for accounting & invoicing alone. Mewayz starts at $69/mo and covers accounting & invoicing, plus HR, projects, support, and more.
See full Mewayz vs FreshBooks →Wave
Free Accounting · $0–$16/mo
Wave gives you free invoicing and basic accounting (with $16/mo payroll add-ons per state). Mewayz at $69/mo replaces Wave plus your CRM, projects, HR, and support tools.
See full Mewayz vs Wave →FAQ
Best Accounting Software for Agencies in 2026 — Common questions
Can Mewayz handle client retainer billing?
Yes — set up monthly retainer subscriptions with hour banks. Each timesheet entry deducts from the client's bank. Overage hours auto-bill at your overage rate.
What about per-project profitability?
Mewayz tracks costs (salary allocation, contractor fees, expenses) per project alongside billed revenue. P&L reports show profit margin per project, client, and time period.
Get the accounting software built for agencies
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