The short answer
For most agencies of 2–20 people, FreshBooks is the best invoicing software in 2026: automatic reminders, deposits, late fees and time tracking are included on every plan. Choose QuickBooks Online if your accountant already works in it, Xero if several people need access or you bill overseas clients, and Harvest if most of your work is billed by the hour. Zoho Invoice is the best free option for low volume.
All 8 tools below can send an invoice and a reminder. They differ on the features that decide whether the money arrives on time: taking a deposit before work starts, adding a late fee, letting the client pay by card or bank transfer from the invoice, and what the price becomes once the introductory offer ends.
Quick comparison
Tool | Best for | Starting price | Automatic reminders | Deposits or part payment | Late fees |
|---|---|---|---|---|---|
FreshBooks | Agencies billing a short client list | $23/month, up to 5 clients | Yes, every plan | Deposits, every plan | Yes |
QuickBooks Online | US agencies whose accountant uses QuickBooks | $38/month | Yes, up to 3 per invoice | Deposits on estimates | Yes, automatic |
Xero | Several users, or clients abroad | $25/month, 20 invoices | Yes, up to 5 per invoice | Part payments recorded | Not documented |
Harvest | Work billed by the hour | $11 per seat/month, plus usage | Yes | Retainer invoices | Not documented |
Productive | Projects, budgets and billing in one place | $12 per user/month | Professional plan and up | Advance-payment invoices | Not documented |
Bonsai | Proposal, contract and invoice in one flow | $25 per user/month for invoicing | Yes, until 16 days overdue | Deposits on proposals | Yes |
Stripe Invoicing | Clients who pay by card or ACH | 0.4% per paid invoice, plus payment fees | Yes | Part payments, once enabled | Not documented |
Zoho Invoice | Free, low volume | $0 | Yes | Part payments | Not documented |
Prices are the regular monthly-billed rates from each vendor’s own pricing page, checked on 28 September 2026, with introductory discounts left out. “Not documented” means the vendor’s own help pages do not describe the feature; it may still exist. Plans change often, so check before you buy.
What the comparison covers
Every tool on this list can produce a clean PDF. The comparison covers the features that change when an invoice gets paid:
Automatic reminders, and whether you can schedule them before the due date as well as after it.
Deposits, so a client commits money before the work starts.
Online payment by card and by ACH or bank transfer, and what each costs you per invoice.
Late fees, applied by the software rather than typed in by hand.
Time and retainers, because most agency invoices are built from one or the other.
The real price for a team, including client caps, per-seat charges and usage fees.
1. FreshBooks: best overall for small agencies
FreshBooks puts the getting-paid features on every plan instead of saving them for the top tier, which is why it comes first here.
Where it works
Automatic reminders, up to 3 before or after the due date, are on all plans, and so are scheduled late fees, deposits, recurring invoices and unlimited time tracking. Clients can pay by card or ACH through FreshBooks Payments, Stripe or PayPal. Client retainers start on the Plus plan.
Where it falls short
The cheaper plans cap billable clients, and archived clients count towards the cap: 5 on Lite and 50 on Plus. ACH payments are for US customers only. Extra team members cost $11 a month each, which adds up quickly for an agency where several people track time.
What it costs
Lite is $23 a month, Plus $43 and Premium $70 on the regular monthly price. Card payments cost 2.9% + $0.30 and ACH costs 1%.
2. QuickBooks Online: best if your accountant already uses it
If your bookkeeper or accountant works in QuickBooks Online, invoicing inside it saves a monthly reconciliation job, and its deposit and late-fee handling is strong.
Where it works
You can request a deposit on an estimate as a dollar amount or a percentage on every plan, and automatic late fees are on every plan too, with a grace period and a choice of flat or percentage charges. Automatic reminders can be set up to 3 times, anywhere up to 90 days either side of the due date.
Where it falls short
Multi-currency invoicing and time entry start on Essentials, and billable expenses need Plus. Clients can pay a deposit online only if you use QuickBooks Payments. Reminders apply only to invoices sent after you switch them on, while late fees can also land on older invoices that are already overdue, so check your open invoices before enabling them.
What it costs
Simple Start is $38 a month. Essentials is $85 and Plus $140. Invoice card payments through QuickBooks Payments cost 2.99% and ACH costs 1%, with a $1 minimum.
3. Xero: best for several users or overseas clients
Xero charges per organisation rather than per user, which makes it the cheapest accounting-grade option once 4 or 5 people need to see the numbers.
Where it works
Automatic reminders are flexible: up to 5 per invoice, before or after the due date, with editable templates. Card and ACH payments run through Stripe or GoCardless, and you can record part payments against an invoice. There are no per-user licence fees on any plan.
Where it falls short
The entry plan allows quotes and 20 invoices, which a busy agency outgrows fast. Multi-currency invoicing and project time tracking are both on the top plan only. Xero’s own documentation does not describe a built-in late fee.
What it costs
Early is $25 a month, Growing $55 and Established $90, billed monthly. With Stripe managed through Xero, US card payments cost 2.9% + 30¢ and ACH Debit costs 1%, capped at $9.
4. Harvest: best for work billed by the hour
Harvest is a time tracker first. If your invoices are hours multiplied by a rate, it removes the step where somebody copies timesheets into an invoice.
Where it works
Tracked time and expenses turn into invoice lines directly. Automatic late-invoice reminders run on a schedule you set, retainer invoices are supported, and it syncs to QuickBooks Online and Xero on paid plans. Clients pay by card through Stripe or PayPal, and by ACH through Stripe on USD invoices.
Where it falls short
Clients cannot pay part of an invoice online. The price is harder to predict than it looks: invoices, projects and clients are billed by usage on top of the seat price, and Harvest’s own example shows a bill moving from $44 to $404. Some billing options also add a Harvest fee to online payments.
What it costs
Teams is $11 per seat a month billed monthly, or $9 billed annually, before usage charges. Stripe’s standard US rates apply to payments.
5. Productive: best for projects and billing in one place
Productive is agency management software: budgets, resourcing, time and invoices in a single tool. It suits an agency that wants profitability per project more than it wants a standalone invoicing app.
Where it works
Time and expenses flow straight into invoices, advance-payment invoices cover deposits, and invoices can show 2 currencies. On Professional you get scheduled reminders, retainer invoicing and accounting integrations.
Where it falls short
The features that matter most for getting paid, reminders and accounting sync, need the Professional plan. Productive’s help centre does not document clients paying an invoice online, so plan on a separate payment route.
What it costs
Essential is $12 per user a month billed monthly, and Professional is $29. Both are cheaper billed yearly.
6. Bonsai: best for proposal-to-invoice in one flow
Bonsai links the proposal, the contract and the invoice, which makes it easy to collect a deposit at the moment the client signs.
Where it works
Deposits can be taken as an upfront payment on a proposal. Late fees apply automatically the day after the due date and repeat monthly, and time entries and expenses attach to invoices. Retainer invoices and multi-currency billing are included from the Essentials plan.
Where it falls short
Automatic reminders stop 16 days after the due date, which is about when a stalled invoice starts needing them most. Accounting sync needs the Premium plan, and the Xero sync skips partially paid invoices and payment fees. Using Stripe or PayPal instead of Bonsai Payments adds a 1% platform fee where Bonsai Payments is available.
What it costs
Essentials, the first plan with invoicing, is $25 per user a month billed monthly, and Premium is $39. Bonsai Payments charges 2.9% + $0.30 for cards and 1% for ACH.
7. Stripe Invoicing: best when clients pay by card or ACH
Stripe Invoicing has no monthly fee. You pay a small percentage when an invoice is paid, which suits an agency whose clients are happy to pay online.
Where it works
Reminders can be scheduled before, on or after the due date on both plans. Payment methods are built in, including cards, ACH Direct Debit and bank transfer, and multi-currency invoicing is supported. Nothing costs you money in a month when no invoice is paid.
Where it falls short
There is no time or project tracking, so something else has to build the invoice. Part payments from the invoice page have to be switched on in your invoice settings, and accounting sync means adding a third-party app. Recurring invoices run through Stripe Billing, which carries its own fee.
What it costs
Starter is 0.4% per paid invoice and Plus is 0.5%, on top of payment fees of 2.9% + 30¢ for domestic cards and 0.8% for ACH Direct Debit, capped at $5.
8. Zoho Invoice: best free option
Zoho Invoice is free, with no paid tier, and it covers more of the essentials than most free tools.
Where it works
Automatic reminders, recurring invoices and part payments are all included, and unbilled time and project expenses can be added to an invoice. It connects to Zoho Payments, Stripe, PayPal and several other processors.
Where it falls short
Invoices are limited to your base currency, and the free plan allows 500 invoices a year, 2 users and 3 projects. Invoices carry Zoho branding, and ACH through Zoho Payments is available on request rather than by default.
What it costs
$0. Zoho Payments charges 2.9% + 30¢ for domestic cards and 0.8% for ACH, capped at $5.
What invoicing software cannot do
Automatic reminders work on invoices that were forgotten. An invoice waiting on an approver, a purchase order or a supplier record receives the same polite reminder on day 7, day 14 and day 21, and stays exactly where it is. 6 of the 7 reasons clients pay late are blockers of that kind, and no setting in any tool above clears them.
2 things help whichever tool you pick. Send invoices from a shared billing address to the client’s accounts payable inbox, so they reach the people who process them. And give one person responsibility for the invoices that reminders do not move, which is a separate decision covered in who should follow up your unpaid invoices.
Collected42 works alongside whatever invoicing software you already use, for $490 a month and up to 10 active payment threads. The cost worth naming: it adds a person to the thread, so it only pays for itself on invoices large enough that their lateness affects your cash flow.
How to choose
Your accountant already works in QuickBooks Online or Xero: invoice there, and add Harvest if you bill by the hour.
You have fewer than 50 clients and want everything included on one plan: FreshBooks.
Your invoices are built from timesheets: Harvest, or Productive if you also want budgets and resourcing.
You want the deposit collected when the proposal is signed: Bonsai, or QuickBooks Online with deposits on estimates.
Your clients pay by card or ACH and you want no monthly fee: Stripe Invoicing.
You send fewer than 500 invoices a year in one currency and want to pay nothing: Zoho Invoice.
FAQ
What is the best invoicing software for a small agency in 2026?
FreshBooks is the strongest all-round choice for a 2–20 person agency, because automatic reminders, deposits, late fees and time tracking are on every plan. QuickBooks Online and Xero are better choices when your accountant already uses them, and Harvest is better when most work is billed by the hour.
Which invoicing software sends automatic payment reminders?
All 8 tools in this comparison can. The differences are in the detail: Xero allows up to 5 reminders per invoice, QuickBooks Online and FreshBooks up to 3, Bonsai stops 16 days after the due date, and Productive includes reminders from its Professional plan.
Can clients pay a deposit through invoicing software?
Yes, in several of them. FreshBooks includes deposits on every plan, QuickBooks Online lets you request a deposit on an estimate, Bonsai takes an upfront payment on a proposal, and Productive and Harvest use advance-payment or retainer invoices.
Is there free invoicing software good enough for an agency?
Zoho Invoice is free and includes reminders, recurring invoices and part payments. Its limits are 500 invoices a year, 2 users, 3 projects and a single currency, which suits a very small agency and rules it out for most growing ones.
Does invoicing software get invoices paid faster?
It speeds up invoices that are late because they were forgotten, or because paying was inconvenient, by adding reminders and a payment button. It does not move an invoice that is waiting on internal approval, a purchase order or supplier setup at the client, which is the more common reason B2B invoices run late.
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