Taking card payments on invoices through Stripe: what to set up and what it costs
- Stripe charges 1.5% plus 20p per transaction for standard UK cards and 1.9% plus 20p for premium or corporate cards, which many B2B customers use.
- Decide which customers receive a pay-now link before you start - new accounts and slow payers benefit most, while established accounts with high invoice values are usually better served by bank transfer.
- Stripe's standard payout schedule settles funds two to seven business days after a card payment, so a paid invoice does not mean same-day cash.
- A dedicated Stripe clearing account in your accounting package is the cleanest way to reconcile net payouts against gross invoices without creating timing gaps in your ledger.
- Stripe does not refund the processing fee if you later refund an invoice, making it important to factor this non-recoverable cost into your fee policy before enabling card payments by default.
How to add a Stripe pay-now link to B2B invoices: covering how the payment flows from customer click to reconciled ledger entry, what Stripe costs per GBP transaction, which customers to offer it to, and how to reconcile net settlements back to Xero or QuickBooks.
When a customer clicks the pay-now link on a Stripe-enabled B2B invoice, their card details pass through Stripe's payment gateway, Stripe authorizes the charge, and the funds enter a Stripe holding balance. Stripe deducts its processing fee - 1.5% plus 20p for a standard UK card, rising to 1.9% plus 20p for a premium or corporate card - before settling the net amount to your bank account on a rolling two-to-seven business day schedule. That net deposit is what arrives in your bank; the gross invoice amount lives in your accounting package until the payout clears and you reconcile the two. On a £1,000 B2B invoice paid by a standard UK card, Stripe takes £15.20. Paid by a corporate card, it costs £19.20. Understanding that gap before you switch on card payments determines whether you absorb the fee, build it into your pricing, or pass it to the customer.
What Stripe costs on a GBP invoice
Stripe's published UK rates as of July 2026 are 1.5% plus 20p per transaction for standard UK cards, 1.9% plus 20p for premium UK cards, 2.5% plus 20p for EEA cards, and 3.25% plus 20p for international cards. There are no monthly fees or setup costs on the standard plan - you only pay when a transaction processes.
In a B2B context, the card type matters more than it does in consumer transactions. Many of your customers will be paying with company credit cards or purchasing cards, which fall into Stripe's premium category at 1.9% plus 20p. A business that assumes it will always pay the 1.5% headline rate and instead processes mostly corporate cards will pay meaningfully more than expected.
The fixed 20p per transaction also affects how the economics work at different invoice values. At £200, that 20p adds roughly 0.10 percentage point on top of the rate. At £5,000, it becomes negligible. Here is how the numbers play out across typical B2B invoice sizes:
| Invoice value | Standard UK card (1.5% + 20p) | Premium/corporate card (1.9% + 20p) | |---|---|---| | £200 | £3.20 (effective 1.60%) | £4.00 (effective 2.00%) | | £500 | £7.70 (effective 1.54%) | £9.70 (effective 1.94%) | | £1,000 | £15.20 (effective 1.52%) | £19.20 (effective 1.92%) | | £5,000 | £75.20 (effective 1.50%) | £95.20 (effective 1.90%) |
At high ticket sizes - where most B2B invoices sit - the difference between absorbing the fee and not absorbing it is measured in tens of pounds per transaction, not pennies. That is enough to matter on a margin.
Custom pricing
Stripe offers negotiated rates for businesses processing high volumes. If your monthly card volume through invoices exceeds around £20,000, it is worth contacting Stripe to request a custom rate. Even a 0.2 percentage point reduction on 1.5% saves £240 a year on £120,000 of annual invoice volume.
Choosing which customers receive a pay-now link
Not every B2B customer should receive a Stripe pay-now link on their invoice. The decision depends on three factors: invoice value, payment history, and the commercial relationship.
For smaller invoices - under £500, say - the reduction in debtor days from a same-day card payment usually outweighs the processing cost by a significant margin. A customer who otherwise sits at 45 days on a £200 invoice costs you far more in working capital than the £3.20 Stripe fee. Including a pay-now link for these accounts makes clear financial sense.
For larger invoices, the calculus changes. A £10,000 invoice paid by corporate card carries a Stripe fee of around £190. If that customer reliably pays by bank transfer within 28 days, the card fee buys you nothing and costs you £190. Reserve pay-now links for customers with a pattern of slow payment, new accounts on their first few orders, or any invoice where your debtor days data shows the account consistently running beyond terms.
The practical approach is to segment your customer base into three groups: those who always get a payment link (new accounts, slow payers), those who never get one (established accounts with strong payment history and high invoice values), and a middle tier where you offer the option but do not embed it automatically. Review this segmentation quarterly - payment behavior shifts over time, and a customer who started slow may have established a reliable record that no longer warrants the card fee.
Deciding how to handle the Stripe fee
UK law has banned surcharging on consumer debit and credit cards since January 2018. Business-to-business transactions follow different rules: surcharging is permissible in B2B contexts, but it carries relationship risk that most businesses prefer to avoid. The two practical options are absorption and price building.
Absorption means accepting that card payments cost 1.5% to 1.9% more than a bank transfer, treating it as a cost of credit control, and not adjusting the invoice. This approach works well when the invoices receiving a payment link are smaller ones where the fee is proportionally manageable and the gain in cash flow speed is worth it.
Price building means raising your standard prices so that the Stripe fee is covered inside the margin on every job, regardless of how the customer pays. This removes the per-invoice decision, but it means your bank transfer customers effectively subsidize your card-paying ones. Review your quotes to check whether current rates have room to absorb 1.5% to 2% before applying this approach across the board.
A third option works well for businesses with a wide range of invoice sizes: offer a small early-payment discount equivalent to the card fee - for example, 1.5% off for payment by bank transfer within seven days - to customers who pay quickly by transfer. This rewards fast bank payers without penalizing card payers, and keeps the invoice face value consistent across all accounts.
Refund risk
if you process a refund on a card payment, Stripe does not refund the original processing fee. On a £1,000 invoice refunded in full, you lose the £15.20 fee permanently. For businesses with any significant refund rate, factor this non-recoverable cost into your fee absorption calculation before making card payments the default for any customer tier.
Setting up card payments on your invoices
The following steps assume you are connecting Stripe to an invoicing system such as Zigaflow's invoice feature and using Xero or QuickBooks as your accounting package. Complete all seven steps before sending your first card-enabled invoice to a customer.
Connect Stripe to your invoicing and accounting systems
Log into your invoicing platform and navigate to the integrations or payment settings section. Select Stripe and follow the OAuth authorization flow: you will be redirected to Stripe, asked to log in or create an account, and prompted to grant your invoicing platform permission to create payment requests on your behalf. Once authorized, return to your invoicing platform and confirm the connection shows as active. Repeat the process in Xero or QuickBooks: connect Stripe as a bank feed so that payouts and fees import automatically into your accounts package. Both connections need to be live before you send any payment-enabled invoices to customers.
Create a Stripe clearing account in your accounting package
Before processing any live payments, create a dedicated current-asset account in Xero or QuickBooks called "Stripe Clearing" or "Payment Gateway Clearing." This account acts as a staging area: each Stripe payment posts to the clearing account at the gross invoice amount, the Stripe processing fee posts separately as a bank fee or payment processing expense, and the net payout that arrives in your main bank account reconciles against the clearing account balance. Without this separation, the timing difference between the payment date and the payout date creates persistent open invoices and unexplained bank entries that take significant time to untangle.
Tag which customers receive a pay-now link
Using the segmentation logic described earlier, identify the customers who should receive a pay-now link and apply the relevant tag or payment profile in your invoicing system. This step prevents the link appearing automatically on every invoice and gives you control over where card fees apply. Keep a record of your segmentation criteria so that when you onboard a new customer or review an existing one, the decision is based on consistent rules rather than individual judgment each time. Review the list at least quarterly as payment behavior changes.
Configure your invoice template to include the payment link
In your invoicing platform's document template settings, enable the payment link for the customer groups you tagged in Step 3. The link should point to Stripe's hosted payment page for the specific invoice - a unique URL that Stripe generates per invoice, tied to the exact amount, which Stripe marks as paid once the card is successfully charged. Do not manually copy a static Stripe link into your template: static links do not update when the invoice is paid, leaving the invoice status open in your system even after the customer has already paid.
Confirm your Stripe payout schedule and bank account
Log into the Stripe dashboard and navigate to Settings, then Payouts. Confirm that the linked bank account is the correct one and set the payout schedule to automatic. Stripe's standard schedule for established UK accounts releases funds two business days after a successful charge; newer accounts may experience a longer initial hold of up to seven days while Stripe completes its verification. Instant payouts are available at an additional fee and are worth considering when cash flow is under pressure and a large invoice has just been paid by card.
Run an end-to-end test before going live
Before sending live invoices with a pay-now link, use Stripe's test mode and send a test invoice to yourself. Complete a test payment using Stripe's test card numbers. Confirm three things: the invoice status updates to paid in your invoicing platform, the gross payment and the Stripe fee post as separate entries in your clearing account in Xero or QuickBooks, and the net payout entry is ready to reconcile. If any of the three does not behave as expected, fix the account mapping before going live. Correcting a reconciliation error after hundreds of live transactions have processed is far more time-consuming than resolving it during testing.
Reconcile each Stripe payout against closed invoices
When a Stripe payout arrives in your bank account, it represents the net total of all activity in that payout cycle: card payments received, minus Stripe processing fees, minus any refunds issued during the period. In Xero, the Stripe bank feed imports the individual transactions associated with the payout and attempts to auto-match them to the invoices marked as paid, using Stripe charge IDs. Confirm each match and investigate any that do not auto-reconcile - these are usually transactions from a different payout cycle or invoices where the reference did not carry through cleanly. For a payout covering 24 transactions, manual reconciliation typically takes 30 to 45 minutes for an experienced bookkeeper; automating the Stripe-to-Xero feed reduces this to a few minutes of reviewing auto-matches.
Keeping Stripe settlements visible in your reporting
One practical benefit of running card payments through an integrated invoicing system is that every Stripe payment links directly back to the invoice it closed. This makes it straightforward to track your total Stripe fee cost as a line in your management accounts, measure average collection time for card-paying customers against bank transfer customers, and maintain a clean debtor days figure that reflects actual cleared receipts rather than invoices raised.
With Zigaflow's reporting feature, invoice status connects to job records so you can identify which jobs closed on time, which required follow-up, and which customer accounts are drifting. For businesses that also sell online, Zigaflow's ecommerce capability uses the same Stripe connection, and the reconciliation approach outlined above applies identically. The key discipline is reviewing the total Stripe fee cost monthly: if it is growing faster than your revenue, it is a signal to revisit your customer segmentation and push more accounts toward bank transfer as they establish a reliable payment pattern.
Sources
- Stripe fees UK 2026: every published rate explainedMerchantHQ · accessed 2026-09-23
- Stripe Payment Fees Explained: Full Breakdown and Hidden CostsAirwallex · accessed 2026-09-23
- B2B Payment Methods: Overview and SolutionsStripe · accessed 2026-09-23
- Payouts and Reconciliation with Xero and StripeStripe Support · accessed 2026-09-23
- How to Reconcile Stripe Payouts in XeroTheBookkeeper.ai · accessed 2026-09-23
- Stripe Review 2025: UK Fees, Features and AlternativesMerchantSavvy · accessed 2026-09-23