Best Time Tracking and Invoicing Tools for Agencies
Agency time tracking only matters if the hours turn into approved time, accurate invoices, collected payments, and useful margin data. This guide is for agencies that need a billing workflow, not just another timer. We prioritised tools that support the path from work performed to client billing: billable rates, approvals, invoice creation, accounting handoff, online payments, retainers, and profitability reporting. Toggl Track remains the highest-ranked time-tracking pick on AgencySoftware, while Harvest is the clearest time-plus-invoicing option. Teamwork also matters if billing is tied to project delivery. It is not a standalone timer like Toggl Track or Harvest, but it suits agencies that want client work, budgets, retainers, and invoicing in one project platform.
Reviewed by Marcus Taylor · how we score · Last updated 2026-06-30 · compare tools · affiliate disclosure
At a glance
| Tool | Index | Ease | From | Free | Best for |
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Choosing the right tool
Start with the billing workflow, not the timer. Hourly agencies need fast time capture, billable rates, approvals, and a clean invoice handoff. Toggl Track is strongest if adoption is the problem, but it is not the best fit if you want native online payment collection inside the invoice.
Do the invoice maths before you pick Harvest. Harvest is the clearest route from time and expenses to invoices and online payments through Stripe or PayPal Standard. The catch is that processor fees apply, and Harvest may add a small extra fee on some card and ACH payments unless you are on its higher paid tier.
Use Teamwork if billing is part of delivery. Teamwork can connect time logs, expenses, budgets, retainers, and invoices inside the same client-work system. The trade-off is complexity, and richer invoicing features sit above the entry-level plans.
Check free-plan limits against real agency use. Harvest Free is limited to 1 active person and 2 active projects, while Teamwork Free is capped at 5 users and 5 projects. Toggl Track has a more generous tracking feel, but paid plans are where billable rates, QuickBooks handoff, and approvals become useful.
Separate invoicing from payment collection. Toggl Track can send invoices to QuickBooks, and Teamwork can export or sync billing data for accounting workflows. Harvest is the one here with sourced online payment support through Stripe and PayPal Standard.
Budget for profitability reporting if margins are tight. Toggl Track Premium adds profitability analysis and fixed-fee projects, Harvest Enterprise adds profitability reporting, and Teamwork puts deeper budget and margin workflows on higher plans. Cheap plans can track hours, but they may not show where margin leaks.
FAQ
What is the best time tracking and invoicing tool for agencies?
Toggl Track is the highest-ranked time-tracking pick if your main problem is getting the team to track time consistently. Harvest is the better fit if you want time tracking, expenses, invoices, and online payments in one focused workflow.
Is Harvest better than Toggl Track for agency invoicing?
Harvest is stronger for built-in invoicing and online payment collection through Stripe and PayPal Standard. Toggl Track is stronger for low-friction time capture and billable-rate control, but its sourced invoicing workflow is mainly invoice generation and QuickBooks handoff.
Where does Teamwork fit in this list?
Teamwork fits if you want time tracking and invoicing inside a broader client-work platform. It is better for agencies managing projects, budgets, retainers, and client delivery together, but it is heavier than a dedicated timer.
Can free plans handle agency billing?
Usually only for testing or solo use. Harvest Free is limited to 1 active person and 2 active projects, Teamwork Free is capped at 5 users and 5 projects, and Toggl Track’s paid tiers are where key billing features become more useful.
How are the tools in this ranking scored?
We score tools on ease of use, feature depth, how well they scale with client work, and price and value. The same underlying tool data powers our reviews, rankings and comparison pages.