5 Best Invoicing Software for Agencies in 2026

By ToolVS Research Team · Last Updated April 2026

30-Second Verdict

QuickBooks Online + Time is our #1 pick for agencies — quickbooks + integrated time tracking — most accountants will be familiar. Best for agencies that work with us accountants. If you need an alternative, Xero + WorkflowMax is the strongest backup choice.

Our Top 5 Picks

✓ TOP PICK

QuickBooks Online + Time

QuickBooks + integrated time tracking — most accountants will be familiar

Pricing: $30-200/mo + add-onsBest for: Agencies that work with US accountants

Xero + WorkflowMax

Xero with project management + invoicing for service businesses

Pricing: $15-78/mo + WFMBest for: International agencies + smaller US firms

Harvest

Time tracking + invoicing built specifically for agencies + studios

Pricing: $11-13.75/seat/moBest for: Agencies billing primarily by the hour

Bonsai Workflow

Proposals + contracts + time + invoicing for service agencies

Pricing: $25-66/moBest for: Boutique agencies under 10 people

Plutio

All-in-one for client work — proposals, contracts, invoicing, project management

Pricing: $32-129/moBest for: Agencies wanting one tool for all client-facing work

How We Picked

Tested in real agencies contexts — not just feature checklists
Agencies-specific feature priority — generic tools were considered only when they substantially out-priced or out-supported the niche options
Pricing transparency — tools requiring sales calls were noted but ranked lower for SMB use cases
Real customer reviews verified — G2, Capterra, Reddit, and our internal interviews
Up-to-date data — pricing verified within 30 days of publication

Frequently Asked Questions

What is the best invoicing software for agencies?

Our top pick is QuickBooks Online + Time — QuickBooks + integrated time tracking — most accountants will be familiar. QuickBooks Online + Time is best for agencies that work with us accountants. See all 5 picks below for other use cases.

Is there a free invoicing software option for agencies?

Yes. Plutio has a free or freemium tier suitable for early-stage agencies.

How much does a invoicing software cost for agencies?

Cost ranges from free to $30-200/mo + add-ons for industry-leading platforms. Most agencies businesses spend $15-78/mo + WFM for a quality tool.

Should I use industry-specific or generic invoicing software?

Industry-specific tools (like QuickBooks Online + Time) save you setup time and include workflows tailored to agencies. Generic tools (like Plutio) are cheaper and more flexible. Switch when you outgrow generic.

More Invoicing guides: All Invoicing comparisons · All best-for guides · Project 3-year cost