Payments Setup (Admin)

How to enable payments, manage options, and configure financial operations in ClinicOS.

Written By Brendan Baker

Last updated About 10 hours ago

Payments requires an administrator to connect and manage the clinicโ€™s payment provider.


This article covers how to set it up correctly, safely, and in compliance with your internal policies.


1. Connect Your Payment Provider

Where to Go

Admin โ†’ Payment Settings

Steps

  1. Select your payment provider.

  2. Log in using the providerโ€™s account credentials.

  3. Confirm that your business information matches provider records.

  4. Authorize ClinicOS to process payments on your behalf.

  5. Save changes.

Once connected:

  • Credit/debit

  • ACH (if supported)

  • Digital wallets
    become available immediately.


2. Configure Accepted Payment Methods

In Payment Settings, toggle which options your clinic supports:

  • Card

  • Cash

  • ACH

  • Digital wallet

  • Split payments

  • Partial payments

These settings determine what your team sees inside the Payments overlay.


3. Set Deposit & Partial Payment Rules

Configure:

  • Minimum deposit amounts

  • Required deposits for surgeries

  • Pre-visit holds

  • Refund windows

  • Whether partial payments can be used for open invoices

ClinicOS will follow your rules across all workflows.


4. Enable MyPet Payments (If activated or in your package for Your Clinic)

If MyPet Payments is live for your account:

You can enable:

  • Client-side invoice payment

  • Remote approvals

  • Digital signatures

  • Stored payment methods

  • Pre-visit deposits

  • Post-visit settlement

To activate:

  1. Go to Admin โ†’ Payment Settings โ†’ MyPet Payments

  2. Toggle it ON

  3. Review your clinicโ€™s consent, messaging, and invoice-sharing preferences

  4. Save

MyPet interacts directly with Payments & Reconciliation โ€” no extra portals needed.


5. Review & Configure Taxes

Go to:
Admin โ†’ Pricing & Taxes

Set:

  • Standard tax rates

  • Tax-exempt items

  • Service vs. product tax rules

  • Use tax (where applicable)

These rates are applied automatically in Payments.


6. Review Pricing Integration

Pricing in Payments comes directly from:

  • Services

  • Inventory

  • CarePlans

  • CarePlan+ flows

Admins should confirm:

  • No duplicate price entries

  • No hidden bundles

  • No outdated codes

  • Surgery packages match current protocols


7. Enable/Monitor Payment Reconciliation

PawthosX Business Presence & Payment Reconciliation is where your financial data syncs, including:

  • Completed payments

  • Refunds

  • Voids

  • Failed transactions

  • Partial payments

  • Deposits

  • Daily summaries

  • Discrepancies

  • Processor messages

Admins should review this dashboard daily to ensure financial accuracy.


8. User Permissions

Under Admin โ†’ Roles & Permissions, configure:

Staff roles allowed to:

  • Collect payments

  • Apply partial or split payments

  • Process refunds

  • View payment history

  • Edit paid invoices

  • Access reconciliation

  • Access Payment Settings (Admins only)

Staff see only what their role allows.


9. Terminal / Hardware Settings (If Used)

If your connected processor uses terminals or card readers:

You can configure:

  • Terminal pairing

  • Tap-to-pay settings

  • Default tip options (if clinic uses them)

  • Local network syncing

Not all clinics use hardware โ€” MyPet and browser-based checkout reduce the need.


10. Final Checklist Before Going Live

  • โ˜ Processor connected

  • โ˜ Payment methods enabled

  • โ˜ Taxes configured

  • โ˜ Price list verified

  • โ˜ Roles & permissions set

  • โ˜ Reconciliation dashboard reviewed

  • โ˜ Deposit/refund rules set

  • โ˜ MyPet payments (if enabled) configured

Once this checklist is complete, Payments is ready for full use across ClinicOS.

11. PAX Android Terminal Setup & Offline Processing

PAX Android terminals are the recommended hardware devices for ClinicOS. They give clinics a reliable, modern checkout option without tying payment success to internet uptime.

These devices connect directly to your payment processor and integrate with Payments inside ClinicOS.


What PAX Terminals Can Do

1. Secure, Standalone Processing

PAX terminals operate as dedicated payment hardware โ€” fully isolated from the clinicโ€™s workstations.
This reduces local device dependencies and increases checkout stability.


2. Offline Mode for Interrupted Internet

If your clinic temporarily loses internet, PAX terminals can continue accepting card transactions up to a preset offline limit (configurable per clinic through your processor).

  • Transactions are securely stored on the device

  • When the connection returns, the terminal automatically processes the queued payments

  • Staff are not blocked during outages

This ensures that even during:

  • storms

  • ISP outages

  • router failures

โ€ฆyour clinic can continue seeing patients and checking clients out without disruption.


3. Security in Offline Mode

Even when offline:

  • Card data is encrypted

  • Nothing is stored in readable form

  • Offline payments follow the rules set by your processor (amount limits, card-type restrictions, risk controls)

ClinicOS never stores card data.


4. Automatic Syncing

When internet connectivity returns:

  1. The terminal reconnects

  2. Offline transactions begin processing automatically

  3. Payment confirmations appear in ClinicOS after settlement

  4. Any failures surface in Business Presence & Payment Reconciliation for review

No manual re-entry. No double charging.


How to Enable PAX Terminals

Setup Steps

  1. Go to Admin โ†’ Payment Settings โ†’ Terminals

  2. Select Add Terminal

  3. Power on the PAX device and connect it to WiFi or Ethernet

  4. Enter the pairing code displayed on the terminal

  5. Confirm device name and location (exam room, front desk, pharmacy, etc.)

  6. Save

Your clinic may assign:

  • default terminal per workstation

  • shared terminal pools

  • mobile terminals for curbside or room-side checkout


Operational Benefits

  • Zero downtime checkout โ€” continue processing even during internet outages

  • No bottleneck at the front desk โ€” use multiple terminals or mobile terminals

  • Stable, predictable workflow โ€” terminals stay connected even when browsers refresh

  • Fewer failed transactions โ€” terminals handle heavy lifting so workstations donโ€™t