Connect Stripe to Cybooks to get paid online. Customers click a link on your invoice and pay by card, Apple Pay, Google Pay, or Link. The payment, fee, and payout all flow into your books automatically through a Stripe Clearing Account.
What you can do once Stripe is connected
Accept card payments from customers worldwide (Visa, Mastercard, Amex, Discover, Diners, JCB, UnionPay)
Offer Apple Pay, Google Pay, and Link for one-tap mobile payments
Send a payment link on every invoice you share
See every Stripe payment, refund, fee, and payout in your books without manual entry
Auto-categorise Stripe fees and non-invoice income
Auto-create customer records from new Stripe payments
Stripe is pay-as-you-go. There is no setup fee and no monthly cost from Cybooks or Stripe. You only pay Stripe's standard processing fee on each payment you receive.
Connect your Stripe account
You need to be on the Cybooks plan that includes Online Payments. If you do not have a Stripe account yet, Stripe will help you create one during the connect flow.
Go to Settings → Online Payments.
Click Get set up with Stripe.
Complete the Stripe onboarding form. Stripe will ask for your business details, ID, and a bank account for payouts.
When Stripe sends you back to Cybooks, you will see Connect successful.
Screenshot needed: The Online Payments page in Settings showing the "Get set up with Stripe" button and the Cards / Wallets sections below.
The Stripe Clearing Account
When you finish onboarding, Cybooks creates a Stripe Clearing Account in your Chart of Accounts. This is a holding account that mirrors your Stripe balance. Every payment, refund, fee, and payout posts here first, so your bank reconciliation always matches.
How a payment flows through the books
A customer pays a 100 EUR invoice. Stripe charges a 2.50 EUR fee and pays out 97.50 EUR to your bank a few days later.
Step | Posting | Amount |
1. Customer pays | Stripe Clearing Account ← Accounts Receivable | +100.00 |
2. Stripe fee | Stripe Clearing Account → Stripe Fees | −2.50 |
3. Payout to bank | Bank Account ← Stripe Clearing Account | 97.50 |
The clearing account ends at zero for that payment, the invoice is marked as paid, the fee lands in your P&L, and your bank reconciles cleanly.
Currency: Stripe in Cybooks is EUR-only at launch. Payments in other currencies are skipped during sync. Multi-currency support is on the roadmap.
Turn on payment methods
From Settings → Online Payments, you can turn each method on or off:
Cards – Visa, Mastercard, Amex, Discover, Diners, JCB, and UnionPay. Turning Cards on also turns on Apple Pay, Google Pay, and Link.
Apple Pay – one-tap payment on iPhone, iPad, and Mac.
Google Pay – one-tap payment on Android and Chrome.
Link – Stripe's saved-payment shortcut. Returning customers pay with one click.
Screenshot needed: The Cards and Wallets sections on the Online Payments page with each method's toggle in the "On" state.
Stripe Settings
Click Payment Settings on the Online Payments page to open the Stripe Settings modal. This is where you control how Cybooks handles your Stripe payments.
Payout Account
Pick the bank account in Cybooks where Stripe deposits your money. Cybooks uses this to match Stripe payouts with the matching bank deposit and reconcile them automatically.
Automate my fees
When this is on, Cybooks posts every Stripe fee straight to the Stripe Fees account. You never see fee transactions on the reconcile screen. Turn it off if you want to review each fee yourself.
Automate my sales
When this is on, any Stripe payment that is not linked to an invoice (for example, a payment link or a checkout from another tool) is auto-categorised to the Stripe Sales revenue account. Invoice payments are never auto-categorised – they are always recorded against the right invoice.
Automatically create customers
When this is on, Cybooks looks for a matching customer by email or name on every Stripe payment. If no match is found, a new customer is created using the billing details Stripe captured.
Default Tax Rule for Cyprus Customers
If auto-create customers is on, this dropdown sets the tax rule for new customers with a Cyprus billing address. The default is 19% VAT. The tax rule is also pre-selected on the transaction so the journal entry is correct from day one.
Screenshot needed: The Stripe Settings modal showing Payout Account, Automate my fees, Automate my sales, Automatically create customers, and Default Tax Rule for Cyprus Customers.
Send an invoice with a payment link
Every invoice gets a unique shareable link once Stripe is connected.
Open the invoice and click the share icon in the top-right context menu.
Copy the link from the modal and send it to your customer in any channel you like – email, WhatsApp, Slack, anywhere.
Tick Mark as sent if you want the invoice status to switch to Sent at the same time. Untick it later if the link was shared by mistake.
The link works for anyone with the URL – your customer does not need a Cybooks account to pay.
What your customer sees
Your customer opens the link and sees your invoice with a Pay now button. After they pay:
A success modal confirms the payment with a small celebration animation.
The invoice is marked as Paid in Cybooks within seconds.
Stripe sends them a receipt email automatically.
You receive an email and SMS notification that the invoice was paid.
Disconnect Stripe
You can remove Stripe from Cybooks at any time from the Stripe Settings modal:
Open Settings → Online Payments → Payment Settings.
Click Remove Stripe from this Cybooks Account.
Confirm in the dialog.
Important: Disconnecting only stops the link between Cybooks and Stripe. Your Stripe account, your past payments, and your Cybooks history are not deleted.
Frequently asked questions
Why are Stripe fees showing up as separate transactions?
Cybooks uses Stripe Direct Charges, which means Stripe deducts the fee from your connected account. We import the fee as its own transaction so it shows up on the reconcile screen and in your P&L. If you turn on Automate my fees, Cybooks reconciles them silently for you.
What happens if a payout has not landed yet?
The payment sits in your Stripe Clearing Account until Stripe pays out. Once the payout reaches your bank, Cybooks matches it and moves the money out of the clearing account. The clearing balance reflects "money on its way to my bank".
Can I refund a Stripe payment from Cybooks?
Refunds are issued from your Stripe dashboard. Cybooks imports the refund automatically and posts it against the same clearing account, so your books stay in sync.