Managing Invoices, Payments, and Flexible Billing

How PracticeRunner supports manual and automated billing workflows, credit card payments, lower-cost bank transfers, recorded outside payments, invoices, statements, superbills, and CMS-1500 claim form exports.

Getting paid should be clear and workable for the way your practice actually runs. PracticeRunner supports manual and automated billing workflows, including credit card payments, lower-cost bank transfers, saved payment methods, AutoPay, invoices, statements, superbills, CMS-1500 claim form exports, and recorded outside payments such as check, cash, Zelle, or other manual payments.

Payment settings can be managed at more than one level:

• Practice-level defaults determine which payment methods and billing options are generally available.
• Client-level billing settings let you make exceptions when one client needs a different collection policy or payment setup.
• Billing collection can stay manual, run through automatic invoicing, or use AutoPay with a saved payment method.
• Practices can also use per-session discounted pricing for bank transfers or manual payments to encourage lower-cost methods when that fits the practice policy.

Creating Invoices

Invoices are typically generated from appointments.

1. From Calendar: Open an appointment and choose Create Invoice.
2. From Client Profile: Go to the Billing tab and choose New Invoice.

Invoices can be emailed directly to clients, who can pay them online via a secure link.

Accepting Payments

PracticeRunner supports both integrated payment collection and externally recorded payments.

Credit and Debit Cards

Clients can pay invoices securely by card through Stripe. If your billing settings enable it, you can also save a card on file for future automatic charges.

Bank Transfers

Bank transfers are processed through ACH, the U.S. bank-to-bank payment network. They can remain pending for a few business days before the bank confirms the result. That delay is normal for bank-to-bank processing and can be longer around weekends, bank holidays, or when the bank needs extra time to confirm funds or authorization.

Compared with cards, bank transfers are usually slower to settle. They are often a good fit for lower-cost billing, recurring payments, or larger charges, but staff should expect a delay before funds are final.

Bank account connections may incur a one-time verification fee, typically around $1.50, when a bank account is securely linked. This verification fee is generally charged only when the bank account is first connected, not on each invoice payment. Standard bank transfer processing fees still apply to payments.

If your organization has bank transfers enabled in Billing settings, clients can:

1. Pay an invoice directly from the payment link using a bank account.
2. Save a bank account on file during intake, from the client profile, or while paying an invoice.
3. Use that saved bank account for future automatic charges when the client’s collection policy is set to AutoPay.

Some practices use bank transfer adoption strategies such as:

• offering per-session discounted pricing for bank transfers or manual payments
• accepting only bank transfers in some online payment setups
• keeping card payments available at the practice level while limiting them for selected clients

Saved Payment Methods and AutoPay

PracticeRunner can store one or more saved payment methods for a client and mark one as preferred for automatic charges.

• Saved methods are scoped to the Stripe account that will actually collect payment. If billing is routed to a different connected account, the client may need to save the payment method again for that account.
• A preferred saved method is required for session AutoPay or monthly AutoPay.
• The client’s Billing / Payments tab shows which saved method is preferred and whether it needs attention.

Billing contacts

Billing can be handled by someone other than the person receiving care when the case calls for it. For example, a parent may pay for a child's treatment, one partner may handle payment for a couple, each group participant may be billed separately, or a sponsoring organization may pay for a consultation group.

Use billing contacts to keep invoices, payment methods, statements, and payment follow-up tied to the person or organization responsible for payment. Billing access should stay separate from forms, scheduling, messages, or broader portal access unless the practice grants those separately.

For details, see Representatives, Billing Contacts, and Approved Helpers.

Pending and Failed Bank Transfers

Bank transfers behave differently from cards after a charge is submitted.

• A successful submission may still show as bank transfer pending until Stripe confirms final settlement.
• While a bank transfer is pending, PracticeRunner avoids creating duplicate charges for the same invoice.
• If a saved bank account or card fails during automatic collection, PracticeRunner can mark that payment method as needing attention and pause further automatic charges.
• Common bank transfer failures include insufficient funds, a closed account, revoked authorization, or bank-side verification problems.

When a saved payment method needs attention, staff should ask the client to save a replacement payment method or choose a different preferred method before AutoPay resumes.

Externally Recorded Payments

Not every payment happens through PracticeRunner. Staff can record outside payments so invoice balances and payment history stay accurate.

Common outside payment examples include:

• cash
• check
• Zelle
• other manual or externally collected payments

Good Faith Estimates

A Good Faith Estimate is a client-facing estimate of expected charges for care that will not be billed through insurance claims. It is usually appropriate for self-pay clients or other clients who will not submit insurance claims or receive superbills for the care covered by the estimate.

Send a Good Faith Estimate through Share Documents & Forms. PracticeRunner asks you to preview and save the estimate before sending so the client receives a locked snapshot.

Use invoices to request payment, receipts to document payment, superbills for client-submitted out-of-network reimbursement, and CMS-1500 claim exports for insurance claim form preparation. Do not use a Good Faith Estimate as a substitute for a superbill or claim document.

Generating Superbills

If you are an out-of-network provider, your clients may need a Superbill to seek reimbursement from their insurance.

1. Go to the Billing section of a client's profile.
2. Choose the date range you want to include.
3. Choose Create Superbill.
4. Review the PDF, including CPT codes and diagnosis pointers.

For a focused walkthrough, see Superbills for Insurance Reimbursement.

Exporting CMS-1500 Claim Forms

Practices that prepare insurance claims can turn on claim forms in Settings → Billing. Once enabled, invoice pages show a Create claim action.

PracticeRunner builds a claim snapshot from the invoice, client demographics, insurance details, diagnoses, service lines, provider details, and practice billing settings. Staff can review and edit the claim before downloading either a full CMS-1500 PDF or a fields-only PDF for pre-printed CMS-1500 form stock.

CMS-1500 export prepares a downloadable claim PDF. It does not submit claims electronically or manage payer adjudication. For a full walkthrough, see CMS-1500 Claim Form Exports.

Refunds

To issue a refund:

1. Find the paid invoice.
2. Choose Refund.
3. Select full or partial refund.
4. The funds will be returned to the client's original payment method.

Related articles

• Payment Disputes and Chargebacks
• Representatives, Billing Contacts, and Approved Helpers
• Using the Client Portal
• Client and Case Workflow Summary