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    How to Create and Send Invoices in FreeAgent – and Mark Them as Paid

    A step-by-step guide for beginners: raise an invoice, email it to your customer, then match the payment when it lands in your bank.

    By In Front Accounting · Published 21 October 2026

    The short answer

    Create the invoice under Work > Invoicing > Add new invoice, then email it with Send Now or Actions > Send by email ('Mark as Sent' doesn't email it). When the money arrives in your bank feed, explain that bank transaction as an Invoice Receipt against the invoice — don't add a separate manual entry, or the payment is counted twice.

    1. Create an invoice

    1. Go to Work > Invoicing and click Add new invoice.
    2. Choose your customer from the contact list. If they're new, create the contact first — check the name, email address and billing address are right, because these appear on the invoice.
    3. Set the invoice date. This is normally the date you supplied the work or goods.
    4. Set the payment terms (for example 14 or 30 days). FreeAgent works out the due date for you.
    5. Check the invoice number. FreeAgent numbers invoices in sequence automatically — leave it as it is unless you have a good reason to change it.
    6. Add your line items: a clear description, quantity and price for each item or service.
    7. Choose the correct VAT treatment for each line. Only charge VAT if your business is VAT registered and the sale is taxable. If you're not sure which rate applies, ask us before you send it.
    8. Make sure your bank details are shown on the invoice so your customer knows where to pay.
    9. Save the invoice and check the preview before moving on.

    2. Send the invoice by email

    There are two ways to email an invoice from FreeAgent:

    1. If you selected automatic emailing when creating the invoice, click Send Now.
    2. Otherwise, open the invoice from Work > Invoicing, then choose Actions > Send by email.
    3. Select the recipient. Check it's the right person — often your customer's accounts team.
    4. Proofread the email and the attached invoice: customer name, amounts, VAT, due date and bank details.
    5. Click send. The invoice status changes to sent.

    'Mark as Sent' does not email your customer

    Mark as Sent only updates the status inside FreeAgent. Use it only if you've already sent the invoice another way (for example, by post or from your own email). Otherwise your customer won't receive it.

    Worked example: a £120 invoice

    The invoice: you invoice your customer £120 (one line item, not VAT registered) with 14-day terms, and email it using Send by email.

    The payment: a week later, £120 arrives in your business bank account and appears in FreeAgent through the bank feed.

    Matching it: you open the £120 receipt, set the Type to Invoice Receipt, choose that invoice in the Invoice dropdown and click Explain transaction.

    The result: the invoice shows as paid, and the £120 is accounted for once — no manual entry needed.

    Part payments and common problems

    Part payments

    If your customer pays £50 of the £120, explain the £50 receipt against the invoice. It shows as part-paid with £70 outstanding. When the rest arrives, explain that receipt against the same invoice and it becomes paid.

    The payment isn't showing yet

    Bank feeds can sometimes be delayed. Wait for the transaction to appear rather than creating a manual entry.

    A payment doesn't match any invoice

    It may be a combined payment for several invoices, a different amount, or from someone you didn't expect. Check with the customer or leave it unexplained and ask us — don't guess.

    You matched the wrong invoice

    Find the bank transaction you explained to the wrong invoice and choose Remove this Explanation. Then explain the transaction again, this time choosing the correct invoice in the Invoice dropdown. The invoice you picked by mistake goes back to unpaid.

    No bank feed? The manual option

    Only use this if the account has no bank feed and you don't upload statements — for example, a cash payment.

    1. Go to Banking > Bank Accounts and open the right account.
    2. Choose More > Add transaction.
    3. Enter the date and amount received, set the Type to Invoice Receipt and pick the invoice.
    4. Save, then check the invoice status.

    Alternative: add the transaction from the invoice itself

    If the invoice has already been sent, you can open it and choose Actions > Add manual bank transaction instead. FreeAgent will use the bank account shown on the invoice, so check that's the account the money actually went into.

    FAQs

    Does 'Mark as Sent' email the invoice to my customer?

    No. Mark as Sent only changes the invoice status in FreeAgent. Use Send Now or Actions > Send by email if you want FreeAgent to email it.

    My customer has paid but the money isn't in FreeAgent yet. What should I do?

    Wait for the bank feed to bring the transaction in — feeds can sometimes be delayed, so give it a little time. Don't add a manual entry, or the payment will be counted twice.

    What if a customer only pays part of the invoice?

    Explain the receipt against the invoice for the amount actually received. FreeAgent shows the invoice as part-paid until the balance arrives.

    I matched a payment to the wrong invoice. Can I fix it?

    Yes. Find the bank transaction you explained to the wrong invoice, choose 'Remove this Explanation', then explain the transaction again with the correct invoice. The invoice you picked by mistake goes back to unpaid.

    Should I charge VAT on my invoice?

    Only if your business is VAT registered and the sale is subject to VAT. If you're unsure which rate applies, ask us before sending.

    Need help? Contact In Front Accounting

    Stuck on VAT, a payment that won't match, or setting up invoicing? Call 01277 549101 or send us a message.

    Book a free call

    Sources

    Menu names reflect FreeAgent's help articles at the time of writing and may change. General guidance, not advice on your specific circumstances.

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