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Manage Invoice Payments

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Updated at Apr 08, 2026
By Kali Patrick

Table of Contents

Prerequisites Where You Can Initiate Payments Take a Full or Partial Payment Take an Overpayment for Credit Split Payments Across Multiple Invoices Take a Quick Payment Process “Bad Debt” Apply Store Credit to an Invoice

Related Docs

  • About Payment Processor Integrations
  • Manage Payment Methods
  • Create an Invoice
  • Work with Store Credit

Syncro provides multiple ways for you to apply payments to open invoices. You can take full or partial payments, take an overpayment (for Store Credit), and split payments across multiple invoices. You can even apply funds to multiple invoices from a single screen.

Prerequisites

Before you can accept payment for an invoice, you must define your available Payment Methods. Some of these may require additional set up. 

See Payment Methods and About Payment Processor Integrations for details.

Where You Can Initiate Payments

There are multiple places inside Syncro where you can initiate taking a payment. These include:

  1. From an Invoice's Details Page, by clicking the Take Payment button:
  2. From an Organization's Details Page by:
    1. Clicking the Make Payment button in the Overview section:
    2. Selecting “Payment” from the New dropdown menu:
  3. From the Global New (+) Menu by selecting “Payment”:

Take a Full or Partial Payment

Notes: 

  • These instructions assume you have already created an invoice and have at least one line item charge on it.
  • If the Organization has multiple open invoices, Syncro lists them all. This means you can apply payments to multiple invoices from a single screen as seen in step 3. See also Split Payments Across Multiple Invoices.

To take a full or partial payments, follow these steps:

  1. Navigate to the Invoices tab.
  2. Click the hyperlinked number of the invoice to open the Invoice's Details Page.
  3. At the top, click Take Payment:

Using Syncro Payments

Syncro displays a New Payment page that looks something like this:

In the Select Open Invoices section at the top, any checked boxes prefill the Amount to Apply with the full invoice balance due, and any checked boxes are added to populate the Payment Amount field in the Payment Details at the bottom. The invoice you clicked Take Payment from automatically has its box checked. 

Note: When there is more than one open invoice for an Organization, all are listed. If you arrive here from any path other than a specific invoice, no rows are checked by default. 

  1. Verify the amounts. Or, change the Amount to Apply (using the Edit icon) to take a partial payment.
    Note: Stripe requirements dictate that $0.50 is the minimum amount 
  2. Complete the Payment Details section:
    1. Verify the Payment Date and select the “Credit Card” Payment Method.
    2. If your client has a stored Payment Profile select it.
    3. Optionally, add a Check/Reference Number.
  3. If you haven't selected a stored payment profile, click Payment Confirmation and enter the credit card information on the Payment Confirmation page.
  4. Click Take Payment. You'll see a success page:
  5. Click Continue.
 
 

Using Other Payment Integrations

If only one invoice is open for the Organization, the New Payment page looks something like this:


If you have multiple open invoices for an Organization and you take a payment, Syncro displays the New Payment page showing all OPEN INVOICES at the top. The invoice you clicked Take Payment from has its “Received” box checked, and the “Amount to Apply” field is prefilled for a full payment:

  1. In the “Payment Amount” field (or "Amount to Apply" field when there are multiple invoices), verify the amount. Or, you can change it to take a partial payment.
  2. Below the “Payment Date” field, use the second dropdown menu to select a Payment Method:

Notes: 

  • Depending on how your payment integrations/payment methods are configured and what you select, Syncro prompts you for additional information (e.g., enter the credit card number, select a stored Payment Profile, etc.).
  • When you change the payment method to “Cash,” Syncro displays an “Amount Tendered” area to help you calculate any change:
  1. If desired, enter or change any other fields. (For example, you would enter a First and Last Name here if the credit card you're accepting is under a different name.)
  2. Click Take Payment. You'll see a success page:
  3. Click Continue. 
 
 
  1. If Syncro detects an open ticket associated with the invoice, the following screen displays:


    Click Continue to return to the invoice's Details page. Alternatively, click Resolve Ticket to resolve it, or View in New Tab to see the ticket's Details Page.

When you go back to the invoice's Details Page, you'll see that it's marked accordingly (Paid or Partially Paid):

or


The invoice will not be marked as fully Paid until the Organization pays any remaining balance.

Take an Overpayment for Credit

When you take an overpayment on an Invoice, Syncro applies the remainder to the Organization for credit on future invoices.

Note: These instructions assume you have already created an invoice and have at least one line item charge on it.

To take an overpayment, follow these steps:

  1. Navigate to the Organizations tab.
  2. Click the hyperlinked Name of a Customer Organization to open their Details Page.
  3. From the +New button menu, select "Payment:"

Using Syncro Payments

The Organization's Open Invoices display at the top:

Check the box next to an Invoice Number to prefill the Amount to Apply with the full invoice balance due and populate the Payment Amount field in the Payment Details at the bottom. 

  1. Click the Edit icon in the Amount to Apply and change the amount to be more than the Invoice Balance Due.
  2. Complete the Payment Details section:
    1. Verify the Payment Date and select the “Credit Card” Payment Method.
    2. If your client has a stored Payment Profile select it.
    3. Optionally, add a Check/Reference Number.
  1. If you haven't selected a stored payment profile, click Payment Confirmation and enter the credit card information on the Payment Confirmation page.
 
 

Using Other Payment Integrations

The Organization's Open Invoices display at the top:

  1. Check the “Received” box to prefill the "Amount to Apply" field with the full amount. (In this example, the full payment amount would be $600.)
  2. Below the “Payment Date” field, use the second dropdown menu to select a Payment Method.
  3. In the “Payment Amount” field, enter the overpayment amount. (In this example, the overpayment amount is $800. This means $200 will remain as future customer credit.)
 
 
  1. Click Take Payment. You'll see the success page.
  2. Click Continue. The invoice shows the invoice as paid:

When you navigate back to the Organization's Details Page and scroll to the Payments section, you'll see the amount paid:



When you click the caret to expand the row, you'll also see the amount applied to the invoice and the overpayment amount as store credit.

Split Payments Across Multiple Invoices

An Organization can have multiple open Invoices, each with a different balance due. When you take a payment, you can decide to split that payment across them.

After you click Take Payment on a specific Invoice, the New Payment page displays:

Using Syncro Payments

In the Select Open Invoices section at the top, the invoice you clicked Take Payment from automatically has its box checked and the Amount to Apply prefills with the full invoice balance due.

For this split payment example, let's the Organization wants to pay $190. To split this across two open invoices, check the box next to the second invoice, and edit the Amount to Apply.

The total Payment Amount updates to $190, and you can click Payment Confirmation (or if using a stored Payment Profile , Take Payment) to proceed.

Tip: The Unsettled Payments report (available under Admin > Reports in the Payments section) can help you track these:

 
 

Using Other Payment Integrations

At the top you'll see the amount (for the Invoice you clicked Take Payment from) that's due. Syncro automatically checks the "Received" box in the relevant row for that invoice, adding the full balance of the invoice to the "Amount To Apply" field by default.

However, each Open Invoice for this Organization has a row with some information about the Invoice, including its Invoice Number, Date, and Balance Due. 

For this split payment example, let's the Organization wants to pay $715. To split this across two open invoices, check the “Received” box next to the second invoice and the total Payment Amount will update:

If the amounts don't exactly match, you can adjust the Amount to Apply and leave the Received box unchecked.

Click Take Payment to process the payment.

Tips: 

  • Click the box in the “Received” header row to check/uncheck all the boxes and apply/remove the payment to/from all open invoices.
  • The Unsettled Payments report (available under Admin > Reports in the Payments section) can help you track these:
 
 

Take a Quick Payment

Notes: 

  • Quick Payments automatically use the first Payment Method you've defined in Syncro.
  • Quick Payments are not recommended for non-Admin users. That's because Taking a Full Payment also captures the specific Payment Method and prompts you to close a Ticket if necessary. 
  • Quick Payments are marked with the generic Payment Method: “Quick.” 
  • Quick Payments can be disabled in Invoice Settings (by unchecking the “Disable Quick Payments Button” box).

To take a quick payment:

  1. Navigate to the Invoices tab and then open an invoice.
  2. Select “Quick Payment” from the Actions button menu:

    The invoice is immediately marked as Paid (in full):

Process “Bad Debt”

Bad Debt happens when an Organization refuses to pay an invoice. 

To track the unpaid invoices, you'll create a payment method named “Bad Debt” with a Payment Type of “Other.”

Then process the invoice as you would any other, using the "Bad Debt" Payment Method. This marks the invoice as Paid and gives you the ability to track these types of invoices.

Apply Store Credit to an Invoice

Store Credits are treated like physical gift cards. If there are multiple credits on file for an Organization, you’ll need to apply them one at a time.

If a customer has Store Credit on file, you can apply that to an invoice as follows:

  1. Navigate to the Invoice.
  2. Click Take Payment.

Using Syncro Payments

Just above Open Invoices (to the right of “Customer Credit Balance”) click Apply:

  1. Change the Amount to Apply if needed.
  2. Click Apply Payment or Apply And Next. The Store Credit is applied to the invoice.
 
 

Using Other Payment Integrations

  1. Just above Open Invoices (to the right of “Customer Credit Balance”) click “Apply:”

    IMPORTANT: Be sure to click the “Apply” link to apply store credit. Clicking Take Payment at the bottom of the page here can result in unwanted duplication of store credit.
  2. Change the Amount to Apply if needed.
  3. Click Apply Payment or Apply And Next. The Store Credit is applied to the invoice.
 
 

Alternatively, you can apply Store Credits from the Organization Details Page's Payments section:

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