By Nicole Harris, online-payments support lead with 9 years of experience troubleshooting invoice, card, and bank-transfer transactions
Last reviewed: July 22, 2026
FreshBooks business users sign in to configure invoice payment methods and review transactions marked Succeeded, Declined, Pending, Refunded, or Charged Back. Clients normally pay through the invoice link sent by the business and do not need access to the owner’s accounting account.
This independent guide is not affiliated with FreshBooks.
Find the transaction before retrying it. A missing payment button, declined card, pending ACH transfer, partial payment, and delayed payout represent different stages of the FreshBooks payment workflow.
What FreshBooks Online Payments Do
FreshBooks is cloud accounting and invoicing software for small businesses and independent professionals. Businesses can connect supported payment gateways and allow clients to pay invoices by available methods such as cards, ACH bank transfers, PayPal, Direct Debit, or eligible Buy Now, Pay Later options. Availability varies by business country, invoice currency, gateway, and account setup.
The invoice determines what the client sees.
A business can establish default payment settings, then change the gateway or supported methods on an individual invoice. FreshBooks also lets the business decide whether partial payments are permitted for that specific document.
Payment collection has several stages:
- The client opens the invoice.
- The client chooses an offered method.
- The processor accepts, declines, or holds the transaction as pending.
- FreshBooks updates the invoice and transaction record.
- An eligible processed balance is included in a payout.
- The receiving bank posts the payout.
A paid invoice and a completed bank deposit are not the same event.
Choose the Correct FreshBooks Route
| Your task | Correct starting point |
|---|---|
| Manage invoices and payment options | FreshBooks business login |
| Recover account access | Forgot Your Password? |
| Pay an invoice as a client | Invoice email and View and Pay Invoice |
| Enable cards or ACH | Online Payments settings |
| Allow a smaller payment | Invoice’s partial-payment setting |
| Split billing across dates | Payment Schedule |
| Review a failed transaction | Payments > Online Payments |
| Check a pending bank deposit | Online Payments and Payouts |
| Correct an offline payment | Add or edit the invoice payment |
| Return money to a client | Supported refund workflow |
FreshBooks’ login guidance covers direct credentials, Google and Apple sign-in, client accounts, and six-digit authentication codes. Repeated failed attempts can temporarily lock the account.
Do this first: identify whether the person is the business user or invoice recipient. Skip creating a FreshBooks business account when the only task is paying an invoice.
Log In to the Correct Business
Open FreshBooks through its company website and use the sign-in method already connected to the account. A person with access to several FreshBooks businesses should confirm the active company before changing a gateway or reviewing a client payment.
A successful login can expose the wrong books.
Verify the business name, client, invoice number, currency, balance, and transaction date. Similar invoice totals are not enough when the owner operates multiple companies or sends recurring invoices for the same amount.
FreshBooks recommends typing credentials manually when browser autofill may be inserting an outdated email or password. A Google or Apple password should be recovered through the corresponding provider when that is the normal sign-in route.
Priority one is the established account. Skip creating another profile because a new business will not contain the original invoices, payment settings, transactions, credits, or payouts.
Enable the Right Payment Method
FreshBooks manages connected gateways and default choices through its Online Payments settings. Individual invoices can override those defaults by enabling or disabling online payments, selecting another connected gateway, and choosing supported methods such as card or U.S. bank transfer.
Check both levels.
A gateway can be connected to the business while one invoice has online payments disabled. Another invoice may offer cards but not ACH. A duplicated invoice can also retain the payment choices copied from its source document.
Before sending, review:
- connected gateway;
- card-payment checkbox;
- bank-transfer availability;
- PayPal or Direct Debit where supported;
- partial-payment setting;
- invoice currency;
- remaining balance.
Do not tell the client to refresh repeatedly when the desired payment option was never enabled.
Priority two is the invoice itself. Skip changing the account-wide defaults when only one document needs a different method.
Why a Client Cannot Pay Part of an Invoice
FreshBooks lets businesses activate partial payments on supported invoices. When the setting is enabled, the client can enter an amount smaller than the outstanding balance. When it is disabled, the client is prompted to pay the applicable full balance or scheduled installment.
A partial payment is not a payment schedule.
Partial payments let the client choose a smaller amount. A payment schedule divides the invoice into defined installments with selected amounts or percentages and dates. FreshBooks supports up to 12 installments in a schedule.
There are exceptions.
A requested invoice deposit must be paid in full through online payments. Once a payment has been added to the invoice, the business can no longer add a deposit request to that same document.
Buy Now, Pay Later also follows separate rules. FreshBooks states that partial payments and FreshBooks payment schedules are unavailable when the client uses Buy Now, Pay Later because the provider manages its own installment arrangement.
Choose one structure. Skip combining a FreshBooks schedule with a financing provider’s installment plan.
Review a Declined Payment
The business can open:
Payments > Online Payments
FreshBooks provides quick filters for transaction statuses including Succeeded, Declined, Pending, and Refunded. Chargeback activity can appear with its own status as well.
A declined transaction means the attempted payment did not complete. FreshBooks sends an account notification when a client’s online payment is unsuccessful.
Do not mark the invoice paid manually.
First compare:
- transaction amount;
- payment method;
- attempt time;
- invoice balance;
- processor;
- current status;
- any newer successful attempt.
A client may try twice after seeing an error. One attempt can remain declined while a later attempt succeeds. Recording another manual payment would then overstate the amount received.
The client may need to check the payment information entered, contact the card issuer, use another method offered on the invoice, or ask the business to enable an alternative. The exact decline reason may not always be available to the business.
Do not ask the client to send payment-card information through email or chat.
Pending Is Not Declined
A Pending transaction has not reached a final successful or failed state. This is common with payment methods that require additional processing, including bank transfers.
Wait for the transaction record to update before asking the client to pay again.
A second attempt can create two legitimate debits if the original pending payment later succeeds. The client’s bank may also display a temporary authorization or pending debit before FreshBooks shows a completed transaction.
Check the FreshBooks status, not a cropped banking alert.
When a pending transaction remains unresolved beyond the processor’s normal window, review the payment inside Online Payments and use the support route shown by FreshBooks. Processing time varies by gateway, payment method, bank, weekends, and holidays.
A pending payment should not be treated as collected revenue until the business’s records support that conclusion.
ACH Bank Transfers Need More Time
ACH payment and payout stages are separate.
The client’s bank transfer must first process as an invoice payment. The resulting FreshBooks Payments balance then becomes eligible for payout according to the account’s processing timeline. The payout must finally be posted by the receiving bank.
This produces a common complaint: “The invoice says paid, but no money is in the bank.”
Review:
- Online payment status.
- FreshBooks Payments balance.
- Payout batch.
- Payout status.
- Destination bank account.
- Bank posting date.
Do not delete and re-enter the invoice payment. That changes the accounting record without accelerating the bank transfer.
FreshBooks’ Payouts area can show balances and payout details for FreshBooks Payments powered by Stripe. Additional balance information is also available through the connected Stripe dashboard.
Check the payout record first. Skip reconnecting the bank unless FreshBooks identifies the destination account or payout connection as the problem.
Client Accounts and Multiple Invoice Payments
Clients can normally pay directly from an invoice without registering for a business account. A primary client may optionally create a client account, save supported payment information, and review documents received from the business.
Client accounts also support paying several outstanding invoices in one action. FreshBooks says the selected invoices are paid simultaneously through Pay Outstanding Invoices.
That can create one larger bank-facing payment covering several FreshBooks invoices.
When the client says the bank amount does not match one invoice, check whether multiple outstanding documents were selected. Review each invoice’s payment history before treating the combined charge as a duplicate.
A secondary contact may receive and pay an invoice but does not necessarily have the same client-account features as the primary client.
Use the invoice link first. Skip troubleshooting full client-account access when direct payment already works.
AutoPay Failure and Retry Status
FreshBooks supports AutoPay for recurring-template invoices and retainers. Clients opt in to automatic charging through a supported card, ACH account, Direct Debit mandate, or PayPal arrangement.
When an automatic charge fails, FreshBooks can place the invoice into a retry workflow. The invoice history may provide Retry Payment after the normal automatic attempts stop.
Check whether FreshBooks is already retrying before collecting another payment.
A manual payment, client-initiated retry, and automated retry can overlap if several people act at once. Review the invoice history and transaction list before using Retry Payment or adding an offline payment.
AutoPay also depends on the recurring invoice setup. It does not automatically apply to every ordinary invoice sent to the same client.
One failed recurring charge does not mean the client’s entire FreshBooks account is locked.
Correct Offline and Overpayments
Money received outside FreshBooks, such as cash, check, or another transfer, can be added to the related invoice so the system recognizes the payment. The business can later edit or delete that manual record when it was entered incorrectly.
Use the actual amount and date.
When the recorded payment exceeds the invoice balance, FreshBooks can create client credit for the excess. That credit may later be applied to another invoice.
Do not reduce the payment amount merely to avoid showing credit if the business actually received more money. The record should match the real transaction.
Refunds follow another route. Deleting or editing a FreshBooks payment does not itself return money to the client. Eligible processor payments require the supported refund workflow, while manually refunded transactions may require a corresponding accounting adjustment.
Correct the books after the real-world payment action, not instead of it.
FreshBooks FAQ
Do clients need a FreshBooks login to pay?
No. They can use the invoice link.
Why is there no partial-payment option?
The business may have disabled partial payments on that invoice. Deposits must be paid in full online, and Buy Now, Pay Later uses its provider’s installment structure instead.
Is Pending the same as Declined?
No. Pending is unresolved; Declined failed.
Why did the client’s bank show a payment that FreshBooks marks pending?
Banks can show temporary authorizations or pending debits before processing finishes. Review the FreshBooks transaction status before requesting another payment.
Can a client pay several invoices together?
Yes. A primary client account can use Pay Outstanding Invoices for selected open invoices.
Why does a paid invoice not appear in my bank?
The payment and payout are separate stages. Review the transaction, available balance, payout batch, destination account, and bank posting status.
Can I retry a failed AutoPay charge?
FreshBooks may retry it automatically first. After those attempts stop, the invoice history can provide a Retry Payment action. Check the current status before initiating another charge.
Does deleting a payment issue a refund?
No. A refund moves money back through the appropriate processor route; deleting or editing a payment changes the FreshBooks accounting record.