The best accounting software for marketing agencies
An agency does not have an accounting problem; it has a project-profitability problem wearing an accounting costume. The question that decides the tool is simple: which retainers and projects actually make money? We reweighted the rubric toward job costing, billable time, and the integrations agencies live inside, then ranked the six that answer it.
For agencies the deciding criterion is project and job profitability — billing a client is easy, knowing which client is quietly losing you money is not. We lifted job costing, billable time, and integration weight; we cut raw scalability. See the full rubric →
Project & job profitability30%
Billable time & expense25%
Integrations (PM / CRM / ads)20%
Value15%
Reporting depth10%
01
RANK
★ Editor’s Choice
QuickBooks Online
Best for agencies
Plus is the tier that matters: project profitability, billable time and expenses, and class tracking let you see margin per client and per retainer, not just total revenue. The ecosystem is the real moat — every PM, CRM and ad-spend tool an agency runs has a native QuickBooks connector. The cost of that ubiquity is price: Plus runs $115/mo and the per-plan user caps push larger shops toward Advanced.
Unlimited users on every plan is decisive for an agency where account managers, a bookkeeper and an external accountant all need access without buying seats. Projects on the Established plan handle time and job costing cleanly. The catch: the project module is lighter than QuickBooks, and you must be on Established ($90/mo) to get it.
For a boutique or solo studio billing by the hour, nothing turns tracked time into a clean invoice faster. Proposals, retainers and client portals are first class. But project profitability is thin — it tells you what you billed, not what the job cost — and the $11/mo per-team-member fee compounds as you hire.
Project tracking, time billing and retainer invoices at a fraction of the price, free under $50k in revenue. The value is real if you live in — or are willing to adopt — the wider Zoho stack for CRM and projects. Outside that ecosystem the integration story is shorter than QuickBooks or Xero.
Overkill for a single agency, the right answer for an agency group consolidating several entities or a roll-up that needs inter-company accounting and revenue recognition. It only makes sense with a finance lead and the budget to match — the base runs around $999/mo before implementation.
Free double-entry accounting and invoicing covers a brand-new shop before the books get complicated. It is on this list to name the trap, not to recommend it for a working agency: no project profitability, no job costing, so you will bill clients without ever knowing which ones pay.
What is the single most important accounting feature for a marketing agency?+
Project and job profitability. An agency runs on retainers and project work, and the failure mode is billing a client steadily while the labour and pass-through costs on that account quietly exceed the fee. A tool that tracks cost against each project — QuickBooks Online Plus, Xero Established, or Zoho Books — surfaces the losing accounts before they sink a quarter. Invoice-only tools cannot.
Is QuickBooks or Xero better for an agency?+
QuickBooks Online Plus wins on project profitability depth and the sheer breadth of integrations with the PM, CRM and ad-spend tools agencies already run. Xero wins when headcount and external access matter, because every plan includes unlimited users while QuickBooks caps users per tier. Most agencies that bill on project margin land on QuickBooks; agencies with many account managers and an outside accountant often prefer Xero.
Why not just use Wave or FreshBooks since they are cheaper?+
Both invoice well, but neither gives you true project profitability. Wave has no job costing at all, and FreshBooks reports what you billed rather than what the work cost. For a solo studio that is fine; for an agency managing multiple retainers it means flying blind on the one number that determines whether you survive.
Do these handle billable expenses and pass-through costs to clients?+
QuickBooks Online, Xero, Zoho Books and FreshBooks all support marking expenses billable and rebilling them to a client or project. QuickBooks and Xero also let you mark up pass-through media or contractor costs, which matters when you front ad spend on a client's behalf.