Agency billing and invoicing, from sent to paid
AgencyPro handles agency billing in the same branded portal where clients send requests and approve work. Create an invoice, email it with a payment link, take payment through Stripe or PayPal, and let reminders and late fees follow up on overdue balances.
What billing in AgencyPro covers
This page covers one-off invoices: project fees, milestones, extra work and anything billed once. You create the invoice, the client pays it online or you record the payment, and the system chases what is late. Invoicing is part of Basic, so it is on every plan.
Retainers work differently. They run as recurring services with automatic charges each period, covered on the retainer and subscription billing page. Fixed-price packages that clients buy at checkout are covered under productized services.
Key facts
- Invoices on every plan, starting with Basic at $39/mo (1 seat included, extra seats $15/mo).
- Clients pay through a payment link: cards, ACH bank transfers and digital wallets via Stripe Connect, or PayPal.
- AgencyPro charges zero transaction fees. You pay Stripe or PayPal processing fees only.
- Seven invoice statuses: Draft, Sent, Viewed, Partially Paid, Paid, Overdue, Cancelled.
- Automatic reminders before, on and after the due date, plus optional late fees after a grace period.
Invoicing and payment tools in the product
Each of these is in the product today. Where it helps, the card names the menu path so you can find it during the trial.
Pick the client, set issue and due dates, add a PO number, notes and terms, then add line items with quantity, rate and tax. Numbers follow your format, for example INV-{YEAR}{MONTH}{NUMBER}. Save as a draft, email it, or download the PDF.
Every invoice email carries a payment link. Connect Stripe to accept cards, ACH bank transfers and digital wallets, or connect PayPal. When the client pays online, the invoice status updates on its own.
Set reminders in Billing > Payment Reminders: pre-due, due date, overdue and a final notice. Each template is editable and includes the payment link, so the client can pay from the reminder itself.
In Billing > Late Fees, choose a percentage or fixed fee, set the grace period in days, and decide whether fees apply automatically or only when you add them. Clients get a notification from a template you control.
Create tax rates with a name, percentage and jurisdiction, and set one as the default. Apply discounts as a percentage or a fixed amount. Taxes show on checkout pages and invoice PDFs.
Turn on manual payments and add named methods, such as "Bank transfer", with the instructions clients see at checkout. Record payments that arrive by bank transfer, check or cash against the invoice. An invoice paid in part shows as Partially Paid until the balance is settled, so it never drops off your list.
How a $6,000 project invoice moves through AgencyPro
A hypothetical example: a 4-person web agency bills a finished site build. The numbers are illustrative; the steps and statuses are the real ones.
Invoices > Create Invoice. Choose the client, set a 14-day due date, and add two line items: Design, 1 x $3,500 and Development, 1 x $2,500. With sequential numbering and the format INV-{YEAR}{MONTH}{NUMBER}, it becomes INV-2026100012.
Email the invoice to the client. It moves from Draft to Sent, then to Viewed once the client opens it. The same invoice sits in their portal next to the project files and messages.
The client clicks the payment link and pays by card or ACH through Stripe, or with PayPal. The status changes to Paid without anyone updating it. If they pay half by bank transfer instead, you record $3,000 and the invoice shows Partially Paid.
If the invoice is still unpaid, a due-date reminder goes out, then an overdue reminder and a final notice. With a 2% late fee and a 7-day grace period, an unpaid $6,000 invoice picks up a $120 fee one week after the due date.
For a checklist of what goes wrong on agency invoices (missing PO numbers, vague line items, no late-fee terms), read invoice mistakes that cost agencies money.
What invoicing costs on AgencyPro
Invoicing is part of Basic at $39/mo, which includes 1 seat. Each extra team member on Basic costs $15/mo. AgencyPro adds no transaction fee to any payment, and clients are unlimited on every plan.
For example, a 3-person agency on Basic pays $39 + 2 x $15 = $69/mo. If the same agency needs time tracking, hourly retainers or credit packs, Pro costs $79 + 2 x $20 = $119/mo.
On a $6,000 invoice, AgencyPro takes $0. Stripe or PayPal charges its standard processing fee, as it would if you invoiced through them directly. Full plan details are on the pricing page.
Where each agency billing job lives
Agencies bill in more than one way. This is where each type of charge is handled in AgencyPro, and which plan you need for it.
| Billing job | Where it lives in AgencyPro | Plan |
|---|---|---|
| One-off project or milestone invoice | Invoices (this page) | Basic and up |
| Monthly or quarterly retainer | Recurring services and subscriptions | Basic and up |
| Retainer with hours or credits included | Hourly or credit-based recurring services | Pro and up |
| Fixed-price package bought online | Service catalog and order forms | Basic and up |
| Prepaid credit packs | Credit packages and portal top-ups | Pro and up |
| Hours tracked against client work | Time tracking and timesheets | Pro and up |
Related pages: retainer billing and subscriptions, service catalog, order forms and checkout, prepaid credit packs, and time tracking and timesheets.
When AgencyPro billing is not the right fit
You need accounting, not invoicing
AgencyPro sends invoices and collects payments. It is not a general ledger, and it does not do bank reconciliation, payroll or tax filing. Keep your accounting software for the books. On Plus, Zapier can pass invoice payments to accounting tools.
You invoice clients in several currencies
Each workspace has a default currency setting. If you bill some clients in USD and others in EUR or GBP, confirm how that would work for your setup before you commit.
Your invoices are built straight from timesheets
Timesheets (Pro) total hours by client and request, and you add those hours to an invoice as line items. If your process depends on turning tracked time into invoice lines in one step, test that exact workflow during the trial.
You send a handful of invoices and need nothing else
If you do not need a client portal, request tracking or file sharing, a standalone invoicing app is cheaper. For a one-off invoice, our free invoice generator or invoice templates may be all you need.
“It replaces the patchwork of tools we used to rely on with one cohesive system. The automated invoicing and payment reminders saved us a ton of time.”
Frequently asked questions
What payment methods can clients use to pay an invoice?
Through Stripe Connect, clients can pay by card, ACH bank transfer or digital wallet. You can also connect PayPal. Payments that arrive another way, such as a bank transfer, check or cash, can be recorded manually against the invoice.
Does AgencyPro take a percentage of payments?
No. AgencyPro charges zero transaction fees on invoices, checkouts and subscriptions. You pay the standard processing fees of Stripe or PayPal, the same as if you used them directly.
How do I bill retainer clients every month?
Set the retainer up as a recurring service with a price per period. Stripe or PayPal charges the client on each renewal, and the client can manage the subscription and payment method in the portal. The recurring billing page covers billing periods, included hours or credits, rollover and trial days.
Can I add sales tax or VAT and discounts to invoices?
Yes. In Workspace Settings > Taxes you create tax rates with a name, percentage and jurisdiction and choose a default. Tax is applied to line items and shown on invoice PDFs and checkout pages. Discounts can be a percentage or a fixed amount.
How do payment reminders and late fees work?
Reminders live in Billing > Payment Reminders. You turn on pre-due, due-date, overdue and final-notice reminders, set the timing and edit the email templates, which include the payment link. Late fees live in Billing > Late Fees: a percentage or fixed amount, a grace period in days, and automatic or manual application.
Can I bill for tracked time?
Time tracking is on Pro and Plus. Your team runs timers or adds manual entries on requests, and Reports > Timesheets totals hours by date, team member, client or request, with a PDF download. You can also sell hourly services that include a set number of hours per purchase or per billing period.
Which plan includes invoicing?
Every plan. Basic costs $39/mo and includes invoicing with Stripe and PayPal, the client portal, project management and messaging, with 1 seat. Extra seats on Basic are $15/mo, so a 3-person agency pays $39 + 2 x $15 = $69/mo. Clients are unlimited on every plan.
Explore more features
Retainer billing
Recurring services with billing periods, included hours or credits, rollover and client-managed subscriptions.
Productized services
Sell fixed-price packages through a service catalog and order forms with add-ons and coupons.
Time tracking
Timers and manual entries on requests, with timesheet reports by client and team member (Pro).
Further reading: how to automate agency billing and invoicing software for agencies, compared.