Navigate to: Client Profile > Financial tab
A client's Credit Balance is a positive amount of money on their account that can be applied toward future invoices. It is separate from their Outstanding Balance, which reflects what they currently owe.
These two balances are independent — a credit balance does not automatically offset an outstanding balance. For example, if a client has a $300 Credit Balance and a $600 Outstanding Balance, the full $600 is still owed. The credit must be actively applied to an invoice to reduce what the client owes.
Shepherd supports three primary credit balance workflows:
Taking a deposit — collecting payment in advance of a visit or procedure
Applying a credit balance — using existing credit to pay an invoice
Refunding a credit balance — returning unused credit to the clien
What You Need to Know
A credit balance and an outstanding balance are not the same thing.
A credit balance does not automatically reduce what a client owes. It must be actively applied to an invoice at checkout.
All invoices should end at $0.00.
A negative remaining balance means a refund or overpayment hasn't been redirected yet and needs to be resolved.
Always confirm the payment screen before clicking Check Out.
Verify the correct amount is applied to the intended invoice. If a client has multiple active invoices, confirm the right one is selected.
Credit balance workflows are available to all Shepherd users, with or without Shepherd Pay.
The Total alone does not confirm a payment is set up correctly.
When using Pay All Invoices, unchecking an invoice row silently shifts its balance into the Credit Amount field. The client is charged the full Total, but that portion becomes a credit balance rather than paying the invoice. Before checking out, confirm the Credit Amount line shows $0.00 unless a credit is intended.
Taking a Deposit
To collect a deposit and add it to a client's credit balance:
Navigate to the client's profile.
Go to the Financial tab.
Click Take Payment.
Select the appropriate Payment Type.
In the Add to Credit Balance field, enter the deposit amount.
If the client has an outstanding balance or open invoices, make sure no invoices are selected.
Click Check Out.
The deposit will appear as a Credit Balance on the client's account. It will not be applied to any invoice until you choose to use it.
Avoiding accidental credit on cash payments: At cash checkout, any overpayment should be recorded as Change Due, not added to the credit balance. Confirm the Add to Credit Balance field shows $0.00 and move the overage to the Change Due field before clicking Check Out. If the overpayment was already recorded as a credit balance, void and re-enter the cash payment correctly, or issue a Credit Balance Refund in cash if the change was already physically handed back to the client.
Applying a Credit Balance to an Invoice
To apply an existing credit balance toward an active invoice:
Navigate to the Active Invoice.
Click Take Payment.
Select Credit Balance as the Payment Type.
Enter the dollar amount to apply.
If the client has multiple active invoices, select which invoice to apply the credit to.
Click Check Out.
If the credit balance does not cover the full invoice total, apply the full credit balance first, then take a second payment for the remaining balance using cash, card, or another method.
If the credit balance does not cover the full invoice total:
1. Apply the full credit balance first, then
2. Take a second payment for the remaining balance using cash, card, or another method.
Refunding a Credit Balance
To return unused credit to the client:
Navigate to the client's profile.
Go to the Financial tab.
Access the refund using either option:
Click the green Credit Balance amount, or
Click More Actions → Issue Credit Balance Refund
In the Refund Credit Balance section:
Select the Refund Method (cash, check, card, etc.) from the dropdown.
If using Shepherd Pay, toggle ON the Shepherd Pay option for credit card refunds.
Enter the Refund Amount.
Click Refund Credit Balance.
The refunded amount will be deducted from the client's credit balance and processed using the selected refund method. You can then choose to print or email a copy of the transaction via the icons below "Receipt" on the subsequent pop-up.
Resolving a Negative Outstanding Balance
A negative outstanding balance means an invoice has been overpaid or adjusted after payment, leaving the client's account showing a negative amount (e.g., -$20.00). Common causes include:
A returned product, medication, or lab that reduced an already-paid invoice
A discount, coupon, or price adjustment applied after checkout
A cash overpayment recorded as credit instead of change due
A duplicate or incorrectly entered payment
A refund already issued but not recorded in Shepherd
Before resolving the balance, confirm which of these caused it — and whether the invoice itself is correct. If the negative balance was created by an invoice or payment mistake, correct the underlying issue first before issuing any refund.
Once confirmed, choose the resolution that fits the situation:
Move the balance to the client's credit account
Use this when the client wants to keep the funds on account for a future visit.
Open the invoice that shows the negative balance.
Click the blue Issue Refund button.
Toggle Shepherd Pay OFF.
Select Credit Balance as the refund method.
Enter the amount.
Click Check Out.
The client will now have a positive credit balance that can be applied to their next invoice.
Refund the balance to the original payment method
Use this when the client wants the funds returned to their card or original payment method.
Open the invoice with the negative balance.
Click Issue Refund.
Select the original payment method (e.g., the card used).
Toggle Shepherd Pay ON if Shepherd Pay should actively process the card refund.
Enter the refund amount.
Click Check Out.
Important: All invoices should be balanced to $0.00. A negative remaining balance on an invoice means the refund has not yet been redirected — follow the steps above to resolve it.
Voiding an Accidentally Added Credit Balance
If a payment was mistakenly added to a client's credit balance, or was duplicated or applied to the wrong client, it can be voided:
Navigate to the client's profile.
Go to the Financial tab.
Under the Payments section, click the three-dot menu (⋮) next to the payment.
Click Void.
Voiding the payment will remove it from the credit balance. If the payment was a duplicate or applied to the wrong account, re-enter the correct payment after voiding. Resolve any remaining negative balance by refunding or moving it to credit balance as appropriate.
Avoid issuing a refund to clear a negative balance caused by a payment error before voiding the duplicate — this can result in double-refunding.
Applying a Partial Credit Balance
A credit balance does not need to be applied in full. To apply only part of the available credit:
Navigate to the Active Invoice.
Click Take Payment.
Select Credit Balance as the Payment Type.
Enter the partial amount you want to apply (not the full credit balance).
Click Check Out.
Take a second payment for the remaining invoice balance using cash, card, or another method.
The unused portion of the credit balance will remain on the client's account for future use.
Transferring a Credit Balance Between Locations
Credit balances in Shepherd are location-specific. A credit balance recorded under one clinic location is not automatically available when viewing an invoice under a different location. This applies to multi-location group accounts with a shared client and patient dataset.
To transfer a credit balance from one location to another, use a custom transfer payment type (set up under your group's payment settings). The general workflow is:
At the source location: Refund the existing credit balance using your clinic's designated transfer payment type.
At the destination location: Add the credit back to the client's account using the same transfer payment type, then use the Pay to Clinic menu to record the payment under the destination location.
The client will now have the credit available at the destination location, where it can be applied to their invoice.
Note: This workflow requires a custom payment method configured for your group. For full setup instructions, see A Group Multi-Location Guide for Transferring Payments. If you are unsure whether your account is configured for multi-location transfers, contact Shepherd Support at (888) 655-8772.
Frequently Asked Questions
Why does a client's invoice still show a negative balance after a refund was processed?
A negative remaining balance on an invoice means the refund has not been redirected to the client's credit balance. To fix this, open the invoice, click Issue Refund, select Credit Balance as the refund method, and click Check Out. This will zero out the invoice and add the amount to the client's credit balance for future use.
Can I apply a credit balance across multiple invoices?
Yes. When taking payment using Credit Balance, you can select which invoice to apply it to if the client has multiple active invoices. If the credit does not cover the full amount of one invoice, apply the available credit first and collect the remaining balance separately.
Can I apply a refund directly to an invoice instead of returning it to the original payment method?
Yes. When issuing a refund, selecting Credit Balance as the refund method will add the refunded amount to the client's account as a credit, rather than returning it to the original payment method (e.g., a card or Venmo). This credit can then be applied to any future or current invoice. This is useful when a client wants to keep the funds on account rather than receive a card refund.
Why is the Check Out button grayed out when I try to move a negative balance to credit?
The Check Out button will be unclickable if an invoice row is selected in the payment screen. When converting a negative outstanding balance to a credit balance, no invoice should be selected — the funds need to flow into the credit balance only, not be applied to a specific invoice. Deselect any checked invoice rows on the payment screen and the Check Out button will become active.
How should split payments be handled to avoid credit balance issues?
When a client is paying with multiple payment methods (e.g., part credit balance, part card), complete each payment type as a separate transaction within the same checkout flow. Apply the credit balance first, then take the remaining amount via the second payment method. Avoid processing partial refunds back to a payment method if the intent was to keep the funds on the client's account — use Credit Balance as the refund method instead to keep the funds accessible in Shepherd.
Why won't Shepherd let me issue a refund, or why does the refund amount reset to $0?
This is usually caused by one of the following:
Wrong refund screen — make sure you are on the correct invoice, not the client's general Financial tab.
No payment selected — you may need to select the specific payment to refund against.
Amount exceeds original payment — Shepherd will not allow a refund greater than the original payment amount.
Shepherd Pay toggle is incorrect — for card refunds that should actively process, Shepherd Pay must be ON. For recording an already-completed refund or moving funds to credit balance, Shepherd Pay must be OFF.
How do I check if a credit balance payment was applied correctly?
The client's Financial tab will display the current Credit Balance in green. Any changes to the credit balance are also reflected in the client's payment history under the Financial tab.