What is the best invoicing software for an agency in 2026?
Six tools ranked to go from tracked hours and signed estimates to paid invoices, for retainers, projects and hourly work.
An agency doesn't invoice like a freelancer. In one month it bills a deposit on a website, hours on a support contract and a flat retainer for SEO. For all three in one app up to about 10 people, FreshBooks is our first pick. If you sell mostly hours, Harvest paired with your accounting app. If your accountant runs on it, QuickBooks Online. Once you pass 5 people, Xero, because it doesn't charge per user. And for a two-person studio, Zoho Invoice is free.
Some links may be affiliate links. The ranking is editorial: a sponsored spot is always labeled on its card, and no affiliate link changes a score.
The best invoicing software for your kind of agency
Time, projects and retainers in one app
Hourly billing$9 per seat per month billed yearly
Your CPA uses itProject profitability on Plus
Growing team, flat billNo per-user fees, $97 on Established
Free for two people500 invoices a year, 2 users
Fixed fees on a budgetUnlimited invoices for $0
6 invoicing tools for agencies compared
The "What matters for an agency" column is the feature that sets each tool apart. Entry prices are misleading: some tools charge per seat, some cap your clients, one charges neither. The cost section below runs the numbers for 5 and 15 people.
| Best for | What matters for an agency | Free plan | Team size | Visit | ||||
|---|---|---|---|---|---|---|---|---|
| 1 | FreshBooks | All-in-one | Time, project billing and retainers in one app | 4.1/5 | Lite $23/mo; Plus $43 | — | 1 to 10 people | Visit → |
| 2 | Harvest | Billable hours | Hours become invoices, synced to your books | 3.7/5 | Teams $9/seat/mo yearly | ✓ | 2 to 15 people | Visit → |
| 3 | QuickBooks Online | Books and projects | Time on invoices from Essentials, project profit on Plus | 4.2/5 | Essentials $85/mo (3 users) | — | 3 to 25 people | Visit → |
| 4 | Xero | No per-user fees | Projects and time on Established, no per-user fees | 4.1/5 | Established $97/mo | — | 5 to 30 people | Visit → |
| 5 | Zoho Invoice | Free | Free, 2 users and 3 projects | 4.0/5 | Free | ✓ | 1 to 2 people | Visit → |
| 6 | Wave | Cheapest invoicing | Unlimited invoices free, no time tracking | 4.2/5 | Starter $0; Pro $19/mo | ✓ | 1 to 3 people | Visit → |
Prices in US dollars as shown by each vendor in 2026, before sales tax. "Billed yearly": monthly price on an annual plan.
Is your tool missing from this page? Email us: hello@hackceleration.com
How we compared and ranked
We started from a real agency, not a solo freelancer: a marketing, design or web shop of 3 to 30 people that bills three ways in the same month. Fixed-fee projects with a deposit and milestones, hourly work, and flat monthly retainers. For each tool we read the official pricing page plan by plan and asked one question: can a signed estimate or a logged hour become a paid invoice without retyping anything?
Then we priced two teams, 5 and 15 people, and read agency threads and user reviews for the complaints that keep coming back: client caps, seat creep, invoices too basic to send. Each tool keeps the same score across all our comparisons. The rank says how well it fits an agency, which is why Harvest, with a lower overall score, sits second: it does the one thing hourly agencies need best. The same logic puts QuickBooks Online (4.2) and Wave (4.2) behind FreshBooks (4.1), and Wave last: Wave has one of our best scores but no link between hours and invoices, the job this page ranks on.
- Hour or estimate to invoice, no retypingTracked time and project budgets flowing into invoices.Heaviest
- Retainers and recurring invoicesFlat monthly fees sent and chased automatically.Heavy
- Cost for a teamPrice for 5 and 15 people, client caps included.Heavy
- Accounting fitBuilt-in books or a clean sync to them.Medium
- Trial and commitmentTrial length, card required or not, monthly or yearly.Medium
- User feedbackRecurring complaints: limits, support, price jumps.Light
Some links may be affiliate links. The ranking is editorial: a sponsored spot is always labeled on its card, and no affiliate link changes a score.
FreshBooks
FreshBooks is the closest thing to a ready-made agency billing app at a small-business price. Unlimited time tracking, project budgets and project billing are on every plan, so a logged hour can land on an invoice without copy-pasting. Retainers, the monthly fee most agencies live on, start on Plus.
The catch is the way it meters you. FreshBooks counts billable clients, not just people: Lite stops at 5 clients, Plus at 50, and only Premium is unlimited. Then each team member beyond the owner adds $11 a month. A 5-person shop with 30 clients lands on Plus at $87 a month ($43 plus four seats at $11).
For agencies the limit to watch is that client cap. Twelve retainer clients and a handful of one-off projects can push you past Lite in your first month, and an agency that grows past 50 active clients jumps to Premium.
- Time tracking and project billing on every plan
- Retainers from Plus
- 30-day trial without a card
- ✓One app from tracked hour to paid invoice
- ✓Easy for non-finance staff
- ✓Clear public pricing
- ✗Client caps: 5 on Lite, 50 on Plus
- ✗$11 for every extra team member
- ✗Less depth than a full agency management tool
Our first pick for an agency of up to about 10 people that wants hours, projects and retainers in one place. Count your billable clients before you pick a plan: that number, not your headcount, usually decides between Plus and Premium.
Harvest
Harvest started as a timer, and that is exactly why agencies keep it. Everyone logs hours against a project, and you turn those hours into an invoice in a few clicks. From Teams up it connects to QuickBooks Online, Xero and Stripe, so the invoice lands in your books and gets paid online.
It is the cheapest way in this ranking to put a whole team on billable time: $9 per seat per month on a yearly plan, $11 month to month. A 5-person team pays $45 a month billed yearly; 15 people pay $135.
A small design studio on a graphic design forum described dropping project tools it found too heavy, moving to Harvest linked to Xero, and finding billing suddenly easy. The trade-off: Harvest's invoices are basic compared with a dedicated invoicing app, so most agencies pair it with QuickBooks Online or Xero.
- The simplest time entry in this ranking
- $9 per seat billed yearly
- Syncs with QuickBooks Online, Xero and Stripe
- ✓Free plan to start
- ✓30-day trial
- ✓Whole team equipped for little money
- ✗Basic invoices next to dedicated tools
- ✗No accounting: you need a second app
- ✗Per-seat price adds up past 15 people
The right pick if hourly work is most of your revenue. Pair it with QuickBooks Online or Xero: Harvest owns the hours, your accounting app owns the books. For 5 people that pairing starts around $104 a month (Harvest at $45 yearly plus Xero Growing at $59).
QuickBooks Online
QuickBooks Online is accounting first, but its middle plans cover what an agency needs to bill. Essentials, at $85 a month for 3 users, adds tracked time to invoices. Plus, at $140 for 5 users, adds project profitability, so you can see whether a fixed-fee site actually made money.
Pricing follows users, in steps. Simple Start is a 1-user plan. At 5 people you are on Plus; past 5 you move up to Advanced at $340 a month. There is no per-seat add-on in between, so a sixth hire can cost you $200 a month.
Its biggest strength for agencies is the ecosystem: Harvest, most time trackers and nearly every bookkeeper connect to it. Its weakness is that it was not built around agency work, so retainers and milestone billing take more setup than in FreshBooks.
- Project profitability on Plus
- Largest integration ecosystem in this ranking
- Accountants know it
- ✓Invoices, time and books in one place
- ✓Works with Harvest out of the box
- ✓Scales to bigger teams on Advanced
- ✗Steep jump from Plus ($140) to Advanced ($340)
- ✗Users capped per plan
- ✗Agency workflows need setup
Pick it if your accountant already works in QuickBooks. For a 5-person agency, Plus at $140 a month covers time and project profit. If you are about to hire a sixth person, price Advanced first.
Xero
Xero's pricing is the opposite of everyone else's here: it does not charge per user. Established, at $97 a month, includes projects, time tracking and multi-currency invoicing, and that price stays the same at 5 or 15 people.
That flat price is why growing agencies like it. Fifteen people on FreshBooks Premium cost $224 a month; on Xero Established, still $97. Multi-currency matters if you bill clients in Canada, the UK or Europe.
Watch the lower plans. Early caps you at 20 invoices, which a retainer agency can hit quickly. Projects and time only come with Established, so Growing alone will not turn hours into invoices; that is where agencies add Harvest.
- No per-user fees
- Projects, time and multi-currency on Established
- Pairs well with Harvest
- ✓Same price at 5 or 15 people
- ✓Strong for clients abroad
- ✓Good value score in our comparisons
- ✗Early capped at 20 invoices
- ✗Projects and time only on Established
- ✗Support is its weakest score
The best value once your team passes 5 people, because the bill does not grow with headcount. Go straight to Established at $97 if you bill hours. If your team already loves Harvest, Growing at $59 plus Harvest is the alternative.
Zoho Invoice
Zoho Invoice costs nothing, and it is not a toy. The free plan covers up to 500 invoices a year, 2 users and 3 projects, enough for a two-person studio billing a few clients a month.
The limits arrive fast for an agency. Three projects is tight once you run several retainers and a site build at the same time, and two users means your third hire has no access. Every invoice also carries a Powered by Zoho Invoice mention, which some clients notice.
Use it as a clean start: proper invoices and project billing from day one. When you outgrow it, the move to a paid tool is easier than moving off spreadsheets.
- Free up to 500 invoices a year
- Projects included
- Part of the wider Zoho suite
- ✓No cost to start
- ✓Proper invoicing from day one
- ✓Room for 2 organizations
- ✗Only 2 users and 3 projects
- ✗Zoho branding on invoices
- ✗Not built for a growing team
Our pick for a two-person studio that wants to stop billing from a template. Plan your exit from the start: by your third hire or fourth active project, you will need FreshBooks or Xero.
Wave
Wave's Starter plan gives you unlimited invoices and estimates for $0. For a small agency that sells fixed-fee projects and flat monthly retainers, that covers the basics: estimate, invoice, reminder, online payment.
Where Wave makes its money is payments. On Starter, card payments cost 2.9% plus $0.60 each. Pro, at $19 a month or $190 a year, adds features and waives the $0.60 on the first 10 card payments each month.
What it does not do is link invoices to tracked hours. If you bill time, you will be copying numbers from a timer into Wave each month, which is exactly the work this page is trying to remove.
- Unlimited invoices on the free plan
- Estimates included
- Pro at $190 a year
- ✓Free to start, no invoice cap
- ✓Simple enough for anyone
- ✓Strong value score
- ✗No link between tracked hours and invoices
- ✗Card fees on every payment
- ✗Thin for a team over 3
A smart pick for a small agency that sells flat fees. If hourly work grows past a few invoices a month, move to FreshBooks, or add Harvest and switch your books to Xero.
What does agency invoicing software really cost?
Every tool here meters something different: seats, users per plan, billable clients, or nothing at all. We redid the math from each official pricing page, per month, for two typical teams.
A 5-person agency with 30 clients
Most commonXero Established costs $97 a month, users included. FreshBooks Plus costs $87 ($43 plus four extra team members at $11), since 30 clients fit under its 50-client cap. Harvest Teams costs $45 billed yearly, but you still need accounting: with Xero Growing at $59, the pair is $104. QuickBooks Online Plus, built for 5 users, costs $140. Zoho Invoice and Wave stay free or nearly free, but Zoho stops at 2 users and Wave doesn't link hours to invoices.
Our take: at 5 people the gap between tools is under $60 a month. Pick on workflow, not price.
- Cheapest full setup
- FreshBooks Plus, $87/mo
- QuickBooks Plus
- $140/mo
A 15-person agency with 80 clients
GrowingXero Established is still $97. FreshBooks needs Premium for more than 50 clients: $70 plus fourteen team members at $11, so $224. Harvest Teams costs $135 billed yearly ($165 monthly), plus your accounting app. QuickBooks Online moves past its 5-user Plus plan to Advanced at $340.
Our take: this is where pricing models decide for you. A flat bill (Xero) or a cheap seat (Harvest) wins; per-user plans with steps (QuickBooks) cost the most.
- Flat price
- Xero, $97/mo
- Highest
- QuickBooks Advanced, $340/mo
Monthly or yearly billing
CommitmentHarvest drops from $11 to $9 per seat on a yearly plan, about 18% off. Wave Pro is $19 a month or $190 a year, about 17% off, roughly two months free. FreshBooks gives you 30 days to try without a card.
Our take: stay monthly for your first full billing cycle, including one retainer run and one hourly invoice. Switch to yearly once you know the tool fits.
- Harvest yearly
- $9 instead of $11
- Wave Pro yearly
- $190
Three ways agencies bill, and the tool that fits each
The right software follows how you sell. Here is what each billing model needs from a tool, and which ones in our ranking handle it without workarounds.
Fixed fee with a deposit and milestones
Websites, launchesYou sell a website build. You bill a deposit at signature, a milestone when designs are approved, and the balance at launch. The tool should start from the estimate so the final invoice subtracts what was already billed.
FreshBooks handles project billing on every plan. QuickBooks Online Plus adds project profitability, so you see whether the fixed fee covered the hours. Tip: track time even on fixed-fee work. It is the only way to price the next project correctly.
- Best fit
- FreshBooks, QuickBooks Plus
Hourly: billing tracked time
Support, consultingOn hourly work the invoice is just the sum of the timesheets, so everything depends on time entry. Send the client the exported timesheet before the invoice; it heads off most disputes.
Harvest turns hours into invoices fastest. FreshBooks tracks unlimited time on every plan, QuickBooks Online adds time to invoices from Essentials, and Xero from Established. Wave and Zoho's free plan are not built for it. Tip: set rates per task type, not per person, so the invoice reads cleanly.
- Fastest
- Harvest
- Not built for it
- Wave
Retainers: a flat monthly fee
Recurring revenueA retainer should go out every month without anyone rebuilding it. FreshBooks handles retainers from Plus, next to the hours and projects of the same client. With Harvest plus accounting, set the retainer up in your accounting app and keep Harvest for the hours.
Tip: write an hours cap and an overage rate into the retainer contract. The tool sends the flat fee; you add the overage from the timesheet on the same invoice.
- Retainers
- FreshBooks Plus and up
One app or a timer plus accounting: how to decide
Most agencies end up in one of two setups. The choice depends less on size than on how much of your revenue is hourly.
One app: FreshBooks
SimplestHours, projects, retainers and invoices live in one place, and your bookkeeper gets access to the same app. It is the simplest setup up to about 10 people, as long as you watch the client cap on your plan.
Two apps: Harvest plus QuickBooks Online or Xero
Hourly agenciesHarvest owns time and invoice drafting; your accounting app owns the books. It costs a little more and adds one sync to watch, but the team gets the easiest timer and finance keeps full accounting. It is the setup a small design studio described in a user thread after dropping heavier project tools.
When to move to agency management software
20+ peoplePast about 20 people, resourcing and margin per project matter as much as the invoice. That is the job of professional services automation tools, which add capacity planning on top of billing. Our agency PSA comparison covers them.
What makes your billing bill creep up, and what to check
Surprises always come from the same places: a client cap you didn't notice, a seat price you forgot to multiply, a plan step at the wrong headcount. Here is what the pricing pages show.
Client caps
FreshBooks counts billable clients: 5 on Lite, 50 on Plus. Zoho Invoice's free plan stops at 3 projects. Count active clients and projects before you pick a plan.
Seat creep
FreshBooks adds $11 per team member, Harvest charges per seat. Not everyone needs invoicing access: ask who only logs time.
Plan steps by users
QuickBooks Online Essentials covers 3 users and Plus 5. A sixth hire means Advanced at $340. Price the next step before you hire.
Invoice caps
Xero Early allows 20 invoices. A retainer agency with 15 clients plus projects hits that in month one.
Payment fees
Wave charges 2.9% plus $0.60 per card payment on Starter. Push bank transfers for large invoices.
Two apps, two truths
With Harvest plus accounting, decide which app is the source of truth for invoices, and turn off duplicate sending.
- Price for next year's team, not today's
- Client and project caps on your plan
- Logged hours flow into invoices
- Retainers on the right plan
- Clean sync with your accounting app
- Card fees vs bank transfer on big invoices
Other tools: unclear pricing, solo focus or time only
These tools come up in agency searches. They are not ranked because their pricing was unclear when we compared, because they target freelancers, or because they only do part of the job.
Bonsai: freelancer roots, growing into agencies
Freelancer focusBonsai bundles proposals, contracts and invoicing, and shows up on most agency invoicing lists. Its plans run from $9 to $49 per user a month billed yearly ($15 to $59 monthly), and Elite needs at least three users. It stays out of this ranking because it was built for freelancers first: every seat is billed, so a 15-person agency pays for creatives who only log hours. We rank it on our freelancer invoicing page instead.
- Status
- Not ranked
Plutio: client portal first
PortalPlutio is an all-in-one workspace with a strong client portal and invoicing inside it. We cover it in our client portal ranking; for invoicing alone, the tools above go deeper.
- See instead
- Client portal ranking
Productive: agency management, confusing pricing
Unclear pricingProductive is a full agency management tool. Its pricing page showed conflicting amounts and does not present invoicing as a standalone feature. We don't publish a price we can't read clearly on the vendor's site.
- Status
- Not ranked
Toggl Track: time tracking without invoices
Time onlyToggl Track is a great timer that we score 4 out of 5. It is not an invoicing tool: use it as the source of hours and connect it to the app that sends your invoices. Some studios start with its free plan and a spreadsheet.
- Role
- Source of hours
Pick your next step based on what you need
Your invoicing tool sits next to your CRM, your timer and your client portal. Here are our other comparisons for agencies.
Which CRMs really bill
Time tracking comes firstBest timesheet softwareTimers compared
You want to run the whole agencyBest agency PSA softwareResourcing, budgets, margin
You bill as a consultantInvoicing for consultantsDay rates and timesheets
You want a branded client spaceBest client portal for agenciesRequests, approvals, invoices
You sell subscriptions at scaleSubscription billing softwareStripe Billing, Chargebee and more
Frequently asked questions
What is the best invoicing software for retainers?
FreshBooks Plus, at $43 a month, if you want retainers next to time and projects in one app. If your retainers are flat fees with no hours attached, Wave's free plan covers the invoicing itself, with unlimited invoices.
Harvest or FreshBooks for an agency?
Harvest if most of your revenue is hourly and you already have accounting software: it has the easiest time entry and costs $9 per seat billed yearly. FreshBooks if you want one app for hours, projects, retainers and invoices, and your client count fits its plan caps.
How do I turn tracked time into invoices?
Log time against a project with a billable rate, then generate the invoice from that project's unbilled hours. Harvest, FreshBooks, QuickBooks Online Essentials and Xero Established all do it. Send the client the timesheet export first: approved hours rarely get disputed.
Per-seat or flat pricing for a 10-person agency?
Flat pricing usually wins past 5 people. Xero Established stays at $97 a month whatever your headcount. On FreshBooks Plus, 10 people cost $142 ($43 plus nine members at $11). On Harvest Teams, $90 billed yearly, plus your accounting app.
What happens when I hit the FreshBooks client limit?
You move up a plan. Lite allows 5 billable clients, Plus 50, Premium unlimited. Agencies with many small retainers hit the Plus cap first, so check your active client count before picking Plus over Premium.
Is there free invoicing software good enough for an agency?
For two people, yes. Zoho Invoice is free up to 500 invoices a year with 2 users and 3 projects. Wave's Starter plan has unlimited invoices for $0 but no link to tracked hours. Beyond two people or a few projects, plan to pay.
Do I need accounting software if I use Harvest?
Yes. Harvest tracks time and drafts invoices, but it does not keep your books. From Teams up it syncs with QuickBooks Online and Xero, so invoices land in your accounting and payments reconcile there.