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Money arrives two ways: somebody hands it over at the desk and you record it, or you send them a link and they pay by card. This page covers both, and how to see what is still outstanding.

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What you’re looking at

Payments sits under Billing in the sidebar. The page is headed Payments Management — “Process and track payments from patients for services, medications, and more” — with Refresh and New Payment in the header, the latter for a payment that is not tied to an invoice you already have open. A new practice sees all three empty. The Pending tab is the one to watch daily: it is your outstanding balance, in your practice’s currency, and it should shrink as you work it.

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Record a payment against an invoice

This is the usual route, because it settles a specific balance.
1

Open the invoice's actions

Find the invoice under Billing → Invoices and select Record Payment. The dialog names what you are settling: “Record a payment for invoice {number} — balance due {amount}”.
2

Check the amount

Amount is prefilled with the balance due. Overtype it for a part payment — the invoice then reads Partially Paid and keeps the remainder outstanding.
3

Choose the method

Payment Method defaults to Cash; the others are Card, Bank Transfer, Mobile Money, Insurance and Other. Set it to what actually happened: the Overview tab breaks takings down by method, and a bank transfer logged as cash quietly ruins that.
4

Add a reference

Reference (optional) takes the transfer reference, cheque number or terminal receipt number — “Transaction / receipt reference”. It is what makes a payment findable when a client queries it three months later. Notes (optional) carries anything else.
5

Select Record Payment

You get a Payment recorded confirmation, and the invoice’s balance drops immediately.
You cannot record more than the invoice still owes. An amount above the balance is refused with “That is more than this invoice still owes. Check whether the payment has already been recorded, then confirm it if you still want to record it.” It is almost always the same payment entered twice — an online payment records itself. If the client really did pay extra, record it from the client’s record with Record payment, which asks you to confirm it first.
Once a payment is recorded against an invoice, that invoice can no longer be deleted — only cancelled. Record against the right invoice: correcting one afterwards is a deliberate, recorded reversal, not a quiet edit.
If the client is not standing in front of you, send them a link and let them pay by card.
1

Open the client's record and start a payment

Choose Send payment link — “Collect payment via a secure link sent to contact”. The Send secure payment link panel opens: “We’ll send a Stripe Checkout link to the patient. They can pay using their card without you seeing their details.”
2

Choose who it goes to

Send to offers the same three choices as sending an invoice: the client’s email on file, A different email, or Both. Choose a different email when someone else is paying — an employer, an insurer contact, a family member — and enter up to three addresses separated by commas.If the client has no email on file, the on-file choices say so and are not selectable; add one to their record, or send the link to a different email.
3

Select Send Link

A toast confirms it went and names every recipient. The email tells the client the link expires in 24 hours, and invites them to reply for a fresh one if it lapses.
Everyone listed gets the link, but the card receipt goes to one address — the client when the client is a recipient, otherwise the first address you entered. That is the address the payment page is prefilled with.
The panel states the cost in the same breath: “A 1.9% platform fee will be auto-deducted from this transaction by Stripe.”
Payment links need a connected payment account under Settings → Online Payments. A practice collecting through Paystack cannot use Stripe links — the product says so: “This clinic collects payments via Paystack — Stripe payment links are not available.” Send your bank details on the invoice instead, via Payment details.

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What the client sees when they pay

After they finish paying, the page tells them one of three things — and it says only what has actually been confirmed with the card network:
“We could not confirm this payment” is not a failure. It means we could not check, so the client is told not to pay again until somebody has looked. If one appears, open the invoice: if the payment arrived it will be there. Ask the client to pay a second time only when you can see the invoice still owes money.
An old link can no longer be mistaken for a new one. Re-sending a link the client has already used, or opening one twice, used to show Payment received whatever had happened — including for an invoice nobody had paid.It now checks first, and says which invoice the payment was for. That matters because a payment link the client has already completed will always take them back to a confirmation page: the payment was real, it was just for a different invoice. Naming it is what stops an old receipt reading as a new one.Links sent before this change show the amount without an invoice number. Send a fresh link rather than forwarding an old email.

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What you are told, and when

Money moving no longer depends on somebody thinking to check the Billing screen. All of these follow your Billing notification preference under Settings › Notifications. Turn that category off and they stop; nothing else changes.
Reminders stop after two. A client who has not paid receives at most two automatic reminders, at least three days apart. After the second, the practice is told and nothing further is sent automatically — the next move is a phone call, not another email.
A payment recorded by hand does not notify anyone. These notices are for money that arrives without anybody at the practice doing something — there is no point telling you about a payment you just typed in yourself.
You cannot send a payment link for an invoice that is already settled, and you cannot send one for more than it owes. The product refuses it rather than taking the money:
  • “This invoice has already been paid in full, so a payment link cannot be created for it.” — the balance is zero. Check the invoice; the payment is probably already recorded.
  • “That amount is more than this invoice still owes. Refresh the invoice and try again.” — somebody paid, or the invoice changed, since the screen was opened. Reload it and the correct balance appears.
Both exist to stop a client being charged twice for the same invoice. To charge a card on file automatically after an appointment rather than asking each time, see Auto Pay.

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Who can do this

Taking money and putting it back are deliberately separate, and voiding is the one that is actually enforced — by the database, not by a toggle. The invite sheet’s Add client payments, Add insurance payments, Refund payments and View Payment Reports switches are recorded against a staff member but read by nothing on this screen. See Staff permissions.

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Check it worked

  • The payment is listed under Payments with the method and the reference you entered.
  • The invoice shows Paid, or Partially Paid with the correct remaining balance.
  • The Pending tab no longer lists that balance.
  • For a payment link: the client received the email, and the payment appears once they have paid.

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Common issues

Overtype it. The prefill is the balance due, not a fixed value, and a part payment is a normal thing to record.
Do not try to delete the invoice — you cannot once it has a payment on it. Reverse the payment and record it correctly. Reversing is a separate permission from adding, so you may need an owner or manager.
Online payments record themselves, but not always instantly. Refresh the Billing page before recording it by hand — recording it manually as well double-counts the money.
You may open the screen but not see the financial figures. Viewing the financial dashboard and viewing payment reports are separate permissions — see Staff permissions.
Fixed. When a clinician orders only some parameters of a lab test, Pending Items now charges what the lab request showed: the sum of those parameters’ prices when every one has a price, and otherwise the test’s own price, once. It used to charge the full test price, and a test ordered one parameter at a time could appear several times. A receipt you open again for a past payment now shows the amount that was actually paid.
Fixed — a test or study ordered against a ward admission (rather than an outpatient visit) could be missing from Pending Items entirely, so its cost could never be collected here. It now appears alongside everything else.

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FAQ

Yes — New Payment on the Payments page. Attach it to an invoice when you can, though; an unattached payment settles no balance and shows up as a reconciliation puzzle later.
Not automatically. Download the invoice PDF, which then shows what has been paid — see Create and send an invoice.
It counts payments recorded in ClinikEHR, not settlements landing in your account. Your provider pays out on its own schedule. See The executive dashboard.