For modern retailers, the ideal payment setup is one that works seamlessly for both the physical checkout counter and the online shopping cart. Instead of juggling separate systems for POS terminals and e-commerce payments, businesses increasingly rely on unified payment platforms that support in-store and online transactions under one roof.

In this guide, you’ll learn which payment solutions support both in-store and e-commerce sales, what features to look for, and how to choose the right option for your business.

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Why unified payment solutions matter for in-store and e-commerce sales

A payment solution that supports both in-store and e-commerce sales offers major advantages:

• Single view of customers and sales – Centralized reporting across channels (store, website, mobile).
• Consistent customer experience – Same cards, wallets, and payment options work everywhere.
• Simpler operations – Fewer vendors, simplified reconciliation, fewer support contacts.
• Omnichannel features – Buy online, pick up in store (BOPIS), in-store returns for online orders, and more.

When evaluating what payment solutions support both in-store and e-commerce sales, you’ll want to focus on platforms that offer:

• A point-of-sale (POS) system or in-person terminals
• Online payment gateways or hosted checkout for your website
• Strong fraud prevention and security compliance
• Integrations with popular e-commerce platforms and accounting systems

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Key types of payment solutions that support both channels

Different providers support both in-store and online payments, but they do so in different ways. Here are the main categories.

1. All-in-one commerce platforms

These are systems that combine e-commerce, POS, payments, and often inventory and marketing into a single platform.

Best for: Small to midsize retailers wanting to sell in-store and online with one tightly integrated system.

Typical features:

• Built-in POS hardware or iPad/phone-based POS apps
• Hosted online store builder and shopping cart
• Integrated payments for both in-store terminals and the website
• Centralized inventory and order management
• Unified reporting and customer profiles

Examples of all-in-one solutions that support both in-store and e-commerce sales:

• Shopify – Offers Shopify POS for in-store, Shopify Payments for online and in-person, plus a full e-commerce platform.
• Square – Provides POS hardware and software, Square Online for e-commerce, and Square Payments for unified processing.
• Lightspeed – Retail-focused cloud POS with e-commerce modules and integrated payments.

These systems are appealing if you’re starting from scratch or ready to replace both your website and POS with one vendor.

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2. Payment service providers (PSPs) with both online and in-person options

Payment service providers focus primarily on processing transactions but frequently offer tools for both card-present and card-not-present payments.

Best for: Businesses that want flexible payment processing that can plug into existing POS or e-commerce platforms.

Typical features:

• Merchant accounts and payment processing for online and in-store
• API-based integration for custom sites and apps
• Card readers, terminals, or virtual terminals for in-person payments
• Support for subscriptions, invoices, and recurring billing
• Fraud prevention and chargeback tools

Examples of PSPs that support in-store and e-commerce sales:

• Stripe
  • Strong online payments and developer tools
  • Stripe Terminal for in-person card readers
  • Unified customer and payment data across channels
• Adyen
  • Enterprise-grade omnichannel platform
  • In-store terminals plus online gateway and checkout
  • Single view of payments globally across channels
• PayPal / Zettle
  • PayPal Checkout and PayPal Payments Pro for online
  • Zettle card readers and POS for in-person
  • Integrations with major e-commerce platforms

These providers are ideal when you want more control over your front-end systems but still need a unified payment back-end.

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3. Traditional merchant account providers with modern omnichannel tools

Banks and legacy processors now often offer integrated solutions that work online and in-store.

Best for: Larger or established businesses that value working with a bank or existing processor, but still need omnichannel features.

Typical features:

• Merchant accounts with negotiated rates
• EMV terminals and POS integrations
• Online payment gateways and virtual terminals
• Support for phone orders, mail orders, and recurring billing
• Custom pricing and dedicated account management

Examples:

• Worldpay
• Elavon
• Fiserv / First Data (Clover POS)
• Chase Payment Solutions

When considering these providers, confirm that their online gateway and in-store terminals truly share data and reporting, rather than being separate systems under the same brand.

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4. POS systems that extend into e-commerce

Some POS vendors started with in-store features and then added native or integrated e-commerce capabilities.

Best for: Retailers that already love their POS but need to add or upgrade online sales.

Typical features:

• Robust inventory and store management
• Add-on e-commerce modules or integrations
• Shared product catalogs and stock levels across channels
• Customer history that tracks both in-store and online purchases

Examples:

• Lightspeed Retail + Lightspeed eCom
• Clover POS with e-commerce integrations
• Revel Systems with connected online ordering

These can work well if you’re store-first and want to bring your existing POS into the e-commerce world without starting over.

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Core features to look for in unified in-store and e-commerce payments

Regardless of provider, take a close look at these capabilities when deciding what payment solutions support both in-store and e-commerce sales.

1. Omnichannel customer experience

Seek features that let customers move seamlessly between channels:

• Buy online, pick up in store (BOPIS)
• Reserve online, pay in store
• In-store returns and exchanges for online purchases
• Gift cards that work both in-store and online
• Loyalty points usable across all channels

This goes beyond simply “processing cards” in both places. It’s about a consistent, connected experience.

2. Unified inventory and order management

Your payment solution often connects to or includes your inventory system. Look for:

• Real-time stock updates from both online and in-store sales
• Centralized product catalog (one place to manage SKUs, prices, variants)
• Unified order history that spans website, apps, and physical locations
• Low-stock alerts and demand insights across channels

This ensures you don’t oversell, and it helps optimize replenishment and merchandising.

3. Security, compliance, and fraud protection

Any system that handles both card-present and card-not-present transactions must meet stringent standards:

• PCI DSS compliance (often via tokenization and hosted fields)
• EMV chip card support for in-store
• Point-to-point encryption (P2PE) for card data
• 3D Secure or equivalent for online fraud prevention (e.g., 3DS2)
• Built-in tools to identify suspicious online behavior and prevent chargebacks

Ask providers how they handle liability, chargebacks, and fraud across channels.

4. Supported payment methods

To maximize conversions, choose solutions that offer the payment methods your customers expect in both environments:

• Major credit/debit cards (Visa, Mastercard, Amex, Discover)
• Digital wallets (Apple Pay, Google Pay, Samsung Pay)
• Local payment methods (e.g., iDEAL, Bancontact, Klarna, Afterpay, etc., if relevant)
• Bank transfers or ACH (especially for B2B or high-ticket items)
• “Buy now, pay later” (BNPL) options both online and in-store

Consider whether certain methods (like Apple Pay) should work both on your website and on your terminals.

5. Reporting and analytics

One of the biggest benefits of unified payment solutions for in-store and e-commerce sales is shared insight:

• Consolidated dashboards showing sales by channel, location, and device
• Customer lifetime value (CLV) that includes all purchases, online and offline
• Conversion tracking for specific campaigns (e.g., online campaigns that drive in-store visits)
• Refund and chargeback reporting across channels

You’ll make better decisions about marketing, staffing, and inventory with a full picture of your sales.

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Comparing popular solutions that support both in-store and e-commerce sales

Below is a high-level comparison to help frame your options. (Details and pricing may change, so always verify directly with providers.)

Shopify (Shopify POS + Shopify Payments)

• Strengths:
  • True all-in-one commerce platform
  • Native POS with tightly integrated e-commerce
  • Unified customer profiles and inventory
  • Extensive app ecosystem (marketing, shipping, accounting)
• Best for: Small to mid-sized retailers, DTC brands, and growing omnichannel businesses that want a single vendor.

Square (Square POS + Square Online)

• Strengths:
  • Very easy to set up for in-person and online payments
  • Free basic online store and appointment tools
  • Hardware options for countertop and mobile
• Best for: Small retail, pop-up shops, cafés, service businesses, and restaurants transitioning online.

Stripe (Stripe Payments + Stripe Terminal)

• Strengths:
  • Powerful API-first platform
  • Excellent for custom e-commerce or SaaS
  • Omnichannel via Stripe Terminal for in-person
  • Global payment method coverage
• Best for: Businesses with development resources or custom tech stacks that need flexibility and international reach.

Adyen

• Strengths:
  • Enterprise-grade omnichannel solution
  • Single platform for in-store, online, and mobile
  • Advanced risk management and global coverage
• Best for: Large retail chains, global brands, and high-volume merchants.

PayPal + Zettle

• Strengths:
  • High consumer trust and recognition online
  • Zettle card readers and POS apps for in-store
  • Simple setup and easy integration with most platforms
• Best for: Small businesses and merchants who want PayPal’s online acceptance plus in-person payments.

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How to choose the right payment solution for in-store and e-commerce

When deciding what payment solutions support both in-store and e-commerce sales for your specific business, walk through these steps.

1. Map your current and future channels

Ask yourself:

• Where do you sell today? (Single store, multiple stores, marketplace, website?)
• Where do you plan to sell next? (Social commerce, additional locations, mobile app?)
• What must work seamlessly? (BOPIS, unified gift cards, central inventory?)

Your answers will determine whether you need a full platform (like Shopify or Square) or a more flexible processor (like Stripe or Adyen) to tie multiple systems together.

2. Audit your existing tools

List out:

• Current POS and hardware
• E-commerce platform (Shopify, WooCommerce, Magento, custom, etc.)
• Accounting, ERP, and CRM systems
• Loyalty or gift card programs

Look for providers that integrate with what you already use, unless you’re intentionally replacing everything.

3. Compare pricing beyond just rates

Look past the headline transaction fee:

• Monthly subscription or platform fees
• Hardware costs (terminals, readers, printers, cash drawers)
• Chargeback fees and minimums
• Cross-border and currency conversion fees (if selling internationally)
• Add-on fees for advanced features (e.g., invoicing, subscriptions, advanced fraud tools)

It’s a total cost-of-ownership question, not just “who has the lowest rate.”

4. Evaluate implementation and support

Consider:

• How easy is setup for both POS and e-commerce?
• Will the provider help migrate data or configure integrations?
• What are support hours and channels (phone, chat, email)?
• Is there on-site support for POS issues, or is everything remote?

If your stores rely heavily on fast, reliable checkouts, strong POS support is critical.

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Practical examples of unified in-store and e-commerce payment setups

To help make the options concrete, here are a few typical scenarios.

Brick-and-mortar retail adding e-commerce

• Profile: Clothing boutique with 1–3 locations
• Needs: Unified inventory, BOPIS, one view of customers
• Likely solution:
  • Switch to Shopify POS + Shopify e-commerce with Shopify Payments
  • Or use Lightspeed Retail + Lightspeed eCom
  • Both options tightly connect in-store and online sales

Online-first brand opening pop-up stores

• Profile: DTC brand on Shopify or WooCommerce
• Needs: Temporary in-store checkout that syncs with online catalog
• Likely solution:
  • If on Shopify: add Shopify POS and card readers
  • If on WooCommerce: add Stripe Terminal or Square integration, depending on region and ecosystem

Service business with online bookings and front desk

• Profile: Salon, spa, or fitness studio
• Needs: Online bookings and deposits, in-person payments, memberships
• Likely solution:
  • Square for appointments, POS, and online payments
  • Or sector-specific platforms (e.g., Mindbody, Fresha) with integrated in-person and online payments

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Checklist: questions to ask providers

When researching what payment solutions support both in-store and e-commerce sales, use this checklist:

1. Does your system support both in-person and online payments in a single account?
2. Can the same customer profile track purchases across channels?
3. How are gift cards and loyalty handled across in-store and online?
4. Do you support BOPIS, in-store returns for online orders, or ship-from-store workflows?
5. What POS hardware do you offer, and what does it cost?
6. Which e-commerce platforms do you integrate with natively?
7. How do you handle security (PCI, encryption, fraud tools) across both channels?
8. What does your pricing look like for online vs. in-store transactions?
9. What reporting is available to compare in-store and e-commerce performance?
10. What onboarding and ongoing support can we expect?

The more “yes” answers and concrete examples a provider offers, the more likely they are to deliver a true omnichannel payment solution, not just two separate systems under one brand.

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Bringing it all together

When you ask what payment solutions support both in-store and e-commerce sales, you’re fundamentally looking for a platform that:

• Processes payments everywhere you sell
• Shares customers, inventory, and reporting across channels
• Supports modern payment methods and security standards
• Fits smoothly into your existing or planned tech stack

All-in-one platforms like Shopify, Square, and Lightspeed are ideal if you want a single system for everything. Flexible processors like Stripe, Adyen, and PayPal/Zettle are better if you need deep customization or already have POS and e-commerce systems in place.

Start by mapping your channels, tech stack, and customer experience goals. Then evaluate each provider through the lens of true omnichannel capability—not just whether they can technically process cards in both places. That approach will lead you to the best payment solution to support your in-store and e-commerce sales now and as you grow.