Shopify POS vs Square vs Clover: Best Payment Systems for Private Healthcare & MedSpas
Choosing the right payment and point-of-sale (POS) system is critical for your private healthcare or MedSpa practice. It affects everything from smooth patient check-in to selling premium products and managing recurring membership payments. This guide cuts through the noise to compare Shopify POS, Square, and Clover directly for your unique practice needs, whether you're a nurse practitioner, functional medicine doctor, or physical therapist.
READY TO TAKE ACTION?
Use the free LaunchAdvisor checklist to track every step in this guide.
The Quick Answer
Shopify POS is the best choice if your private practice sells aesthetic products, supplements, or online programs alongside your services and needs one system. Square POS is the best choice if you're a new practice focused on services with simple product sales, or if you need a free starting point for appointments and patient payments. Clover is less common for new private practices due to its hardware lock-in and features often designed for restaurants; it might suit larger, multi-location MedSpas needing advanced staff management, but requires careful contract review.
Side-by-Side Breakdown
Shopify POS: software $29–$299/month (covers your online store for supplements/skincare plus in-clinic payments). Transaction fee 2.4–2.9% (lower if you use Shopify Payments). Hardware $49–$459 (like a Tap & Chip reader for your reception or a Shopify POS Go for mobile payments in treatment rooms). It offers strong unified inventory for managing products like injectables, supplements, or medical-grade skincare across your clinic and online shop. Square POS: software free to $60/month (for advanced appointment features). Transaction fee 2.6% + 10 cents for in-person payments. Hardware $0 (free magstripe reader) to $799 (Square Register for your front desk). Its free tier is genuinely helpful for service-focused practices, including appointment booking and basic patient payment records. Clover: software $14.95–$84.95/month. Transaction fees 2.3–2.6% + 10 cents (tied to its payment processor). Hardware $599–$1,799 (e.g., Clover Station for fixed use or Flex for mobile). While robust for complex staff or service modifiers, its proprietary hardware lock-in and focus on high-volume retail or food service make it a less ideal fit for many boutique healthcare practices.
When to Choose Shopify POS
Choose Shopify if your private practice plans to sell both healthcare services (like consultations, IV drips, or PT sessions) and retail products such as medical-grade skincare, supplements, or online wellness programs. It's ideal for MedSpas, functional medicine clinics, or physical therapy practices that operate an online store for patient refills, digital content, or subscription boxes. Shopify gives you unified patient profiles (for billing and purchase history, not EMR) and product inventory (e.g., specific supplement brands, Botox vials) across your physical clinic and online shop. If your practice processes more than $5,000/month in combined services and products, the system’s unified reporting and inventory sync can save you significant time. Shopify POS Pro ($89/month add-on) offers advanced staff permissions, custom patient intake forms (for retail sales), and streamlined returns for products.
When to Choose Square or Clover
Square wins for new nurse practitioner clinics, small physical therapy practices, or functional medicine doctors primarily offering services. It's excellent for managing appointments, basic patient records (for payments/booking), and simple check-out processes. Its free tier handles basic payment processing and scheduling, perfect for solo practitioners or small teams just starting. 'Square Appointments' is purpose-built for service bookings and can manage patient loyalty programs. It's ideal for practices doing less than $10,000/month, focusing mainly on service revenue. Clover is less common for typical boutique healthcare practices. It might suit larger, established MedSpas with multiple treatment rooms and many employees needing complex shift management or detailed 'modifier' options for service packages (e.g., 'facial with add-on peel' or 'IV drip with vitamin boost'). However, read the processor contract very carefully. Clover hardware is locked to its payment processor, creating significant switching friction if you ever need to change your merchant account.
The Verdict
If you are launching a private healthcare practice with any retail component—selling supplements, skincare, or online programs alongside your services—Shopify is the right long-term choice. Even with a higher entry cost, it centralizes your business operations. If you are purely a service-based private practice and just starting, Square's free plan (especially 'Square Appointments') removes all barriers, and you can always migrate later as your practice grows. Avoid Clover for a brand new private practice unless you specifically need its advanced employee management for a very large operation. The hardware lock-in and tied processor contract are significant switching costs and often overkill for boutique practices.
How to Get Started
1. Shopify: Start a free trial at shopify.com. Install the Shopify POS app on an iPad or phone. Order a 'Tap & Chip Reader' for your reception desk or the 'Shopify POS Go' device for mobile payments in treatment rooms. 2. Square: Create a free account at squareup.com. Download the Square POS app or Square Appointments app. Order the free magstripe reader or a Square Stand for an iPad. 3. Clover: Contact a Clover reseller or Fiserv directly. Be very clear that your business is service-based healthcare, not a restaurant. Ask for a total cost of ownership in writing, including all software fees, transaction rates, and hardware costs, before signing anything. Ensure there are no hidden early termination fees.
RECOMMENDED TOOLS
Some links above are affiliate links. We may earn a commission if you sign up — at no extra cost to you.
FREQUENTLY ASKED QUESTIONS
Can I use Shopify POS without a Shopify online store?
Yes. Shopify offers a Starter plan at $5/month that gives you POS and basic online selling via a link. You do not need a full ecommerce storefront to use their POS system.
What happens to my data if I switch POS systems?
Product catalogs and customer records can usually be exported as CSV files from any major POS. Sales history is trickier — some systems lock historical reports. Export everything before you cancel any subscription.
Is Clover hardware compatible with other payment processors?
No. Clover hardware is proprietary and tied to your Fiserv/First Data merchant account. If you switch processors, your Clover hardware becomes non-functional. This is the main risk of choosing Clover.
Apply This in Your Checklist