Payments wired into your pharmacy software

We connect payments to the systems you already run so balances, receipts and deposits reconcile automatically. Connect payments to your pharmacy management system and IIAS POS.
Talk to a pharmacy payments specialistAll independent pharmacies solutions
Free 30-minute consultation. Review your setup, compare options and leave with clear next steps.

Payment solutions for independent pharmacies

How each solution supports independent pharmacies

See what each option adds to the way your business takes and tracks payments.

Square Point of Sale

For independent pharmacies: Bring prescriptions, health supplies and pharmacy purchases into a point-of-sale workflow, with reporting organized around prescription charges, eligible items and customer invoices. Square Point of Sale is Square's free POS app for taking payments in person, online and on the go. Front-store checkout for OTC and gift items; Square says in-store pharmacies can process HSA/FSA, but confirm IIAS needs first. Roots Payments, an independent Square Reseller, configures it around how your pharmacy actually checks customers out.
  • Map your services, fees and products into the Square item library before your first customer
  • Recommend and configure Square hardware for your front desk or field work (you buy it from Square)
  • Set team permissions so each role sees only what it needs
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Square Inventory

For independent pharmacies: Track pharmacy retail products, health supplies and customer purchases with item-level stock records and replenishment workflows. Square's item library tracks products, stock and sales across your POS and online store, and Square for Retail features add deeper inventory tools. Track front-store products and seasonal items. Roots imports your catalog and sets up counts and alerts.
  • Import and clean up your product catalog
  • Set stock counts, low-stock alerts and categories
  • Configure barcode scanning and labels
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Merchant Account

For independent pharmacies: Arrange a processing account for prescriptions, health supplies and pharmacy purchases, with checkout methods matched to how customers pay. A dedicated merchant account underwritten for your pharmacy, with pricing you can read and a person to call. A pharmacy account connected to an IIAS-capable, SIGIS-certified pharmacy POS.
  • Analyze your current statements and quote side by side
  • Prepare the underwriting package so approval moves quickly
  • Set up terminals, gateway and software connections
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Custom Payment Integration

For independent pharmacies: Connect the payment flow for prescriptions, health supplies and pharmacy purchases with your software and the operational records behind prescription charges, eligible items and customer invoices. We connect payments to the systems you already run so balances, receipts and deposits reconcile automatically. Connect payments to your pharmacy management system and IIAS POS.
  • Scope integrations your software vendor supports
  • Build and test the connection
  • Keep sensitive data out of payment records

Mobile Payments

For independent pharmacies: Collect payments for prescriptions, health supplies and pharmacy purchases away from a fixed counter, with transactions recorded against the sale or job. Accept cards on a phone or tablet at a client's home, a job site or an event. Take payment at delivery with card readers.
  • Choose devices for your field workflow
  • Set up users and permissions
  • Train staff on offline and signature rules
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Square for Retail

For independent pharmacies: Connect pharmacy retail products, health supplies and customer purchases to a retail catalog, stock tracking and customer purchase history. Square pitches its retail POS as a way to "sell more and stay stocked with a POS designed for retail." Real-time stock, barcode checkout and vendor purchase orders cover the day-to-day of most independent pharmacies. Roots Payments, an independent Square Reseller, sets it up and supports it for independent pharmacies.
  • Recommend the Square plan and device mix for your store size and number of locations
  • Import and clean your catalog: SKUs, variants, barcodes, categories, taxes and vendor costs
  • Set up employee roles, passcodes and permissions before launch
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Square Hardware Setup

For independent pharmacies: Choose and configure Square checkout equipment for prescriptions, health supplies and pharmacy purchases, including counter, mobile and staff workflows. A countertop Register with a scanner and cash drawer, plus a Handheld for the floor, covers most independent pharmacies. Square offers a two-screen Register, a pocketable Handheld with a built-in barcode scanner, the all-in-one Terminal, the iPad-based Stand and a Register Retail Kit with printers, scanners and a cash drawer. We spec, install and test every device.
  • Spec the device mix by lane count, floor size and mobile needs
  • Pair scanners, label printers, receipt printers, scales and cash drawers
  • Set up networking, including a wired backup for the countertop
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Square Loyalty

For independent pharmacies: Create a rewards program around prescriptions, health supplies and pharmacy purchases, with earning rules tied to how customers shop. Square describes loyalty as a way to "reward returning customers and encourage future visits." Regulars drive most of the revenue at independent pharmacies, and points tied to the phone number at checkout keep them coming back. We design the reward rules and set them up at the register and online.
  • Design a reward structure your margins can afford
  • Set up enrollment prompts at checkout and online
  • Import your existing loyalty members where possible
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Square Age Verification

For independent pharmacies: Add age-check procedures to restricted items within prescriptions, health supplies and pharmacy purchases and train staff on the checkout process. Square lets you set age restrictions on items so the POS prompts for age verification at checkout. OTC items with age limits (some cough medicines, nicotine replacement) can be tagged for an ID prompt at checkout. We tag every restricted item and set up ID scanning.
  • Tag every age-restricted SKU and category
  • Set up 2D scanners at every lane
  • Train staff on declines and fake-ID handling
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Custom Payment Integration questions

Questions pharmacy teams ask about patient payments.
A project can connect checkout, payment status, refunds or reconciliation to your business software. Roots scopes the required data flow and builds the agreed connection.
We map the workflow, review API or file documentation and define acceptance checks. You receive a project scope and quote before development starts.
Bring your software documentation, payment workflow and reporting files. Roots uses these details to plan the workflow for independent pharmacies and prepare a clear setup scope.
Request a quote for your business and the setup you need. We review the scope and costs with you before you proceed. Consultations and payment reviews are free.

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Book a free 30-minute review. We’ll map your setup, explain the options and work through clear next steps.
Talk to a pharmacy payments specialistAll independent pharmacies solutions