Retail POS Most “best POS” lists treat online selling as a checkbox. It isn't. A register that syncs badly to your website creates the two failure modes that actually cost money: overselling stock you don't have, and customers who can't return a web order at your counter. This ranking scores the pairing — storefront quality, sync integrity, fulfillment options and the all-in monthly cost of running both channels on one system. Our omnichannel ranking covers the service layer in more depth; this page is the buy-this-for-that-both-places answer, with computed costs.
Facts were read from vendor pages on 2026-11-05 (Square re-verified in full; Shopify carries its 2026-10-22 official USD read after another geo-localised render today, and Lightspeed and Clover carry their 2026-10-29 official reads — see the methodology note at the end). Scoring follows our published eight-criterion methodology.
Quick Picks
Shopify POS
The only system here where the website is the foundation and the register plugs into it: one catalog, two-way sync, pickup/delivery/ship-from-store built in. From $29/mo (annual).
See the breakdown ↓Square
A $0 plan that genuinely includes an online store and pickup/local delivery on the same catalog. The trade: 3.3% + 30¢ online on Free, and retail tooling from $49/mo.
See the breakdown ↓Lightspeed Retail
Best back office of the four, but its retail plans don't include a real storefront — pairing via the official Shopify integration is the common pattern, at two subscriptions.
See the breakdown ↓Clover
Great counter experience, online selling bolted on through App Market apps or a BigCommerce/Shopify connector. Workable, but the sync layer is someone else's product.
See the breakdown ↓The Pairing, Compared
| Shopify POS | Square | Lightspeed Retail | Clover | |
|---|---|---|---|---|
| Our overall score | 4.0 / 5 | 3.8 / 5 | 3.6 / 5 | 3.0 / 5 |
| Built-in online store | Full Shopify storefront — themes, checkout, apps | Square Online on every plan, incl. Free | No storefront on retail plans; eCom in transition | App Market stores; official BigCommerce integration |
| Inventory sync web ↔ store | Automatic, two-way, one catalog | Shared catalog and back office | Only via integrations (official Shopify connector) | Third-party connectors; sync quality varies by app |
| Fulfillment options | BOPIS, local delivery, ship-to-customer, emailed carts | Pickup + local delivery on all plans; preorders on Plus | Verify current state per configuration | Via apps |
| Return a web order in-store | Any location (POS Pro, $89/mo per location) | Supported for Retail sellers | Depends on integration setup | Not verified |
| Online card rate | 2.9% + 30¢ (Basic) | 3.3% + 30¢ Free · 2.9% + 30¢ paid | Set by the platform you pair | App-dependent, unverified |
| In-person card rate | 2.3–2.6% + 10¢ by plan (official)* | 2.6% + 15¢ · 2.5% · 2.4% by plan | 2.6% + 10¢ | 2.6% + 10¢ Starter · 2.3% + 10¢ Retail Growth |
| Software to start both channels | $29/mo (Basic, annual) | $0/mo | $89/mo + storefront platform | From $16/mo (36-mo term) + apps |
* Shopify's card-present rates and plan prices are now read straight from the official US pricing page (2.6% + 10¢ Basic → 2.3% + 10¢ Plus; plans $29/$89/$359 annual — re-verified 2026-11-05, the date we recorded the increase). Square rates re-read from its US pricing page 2026-11-05. Lightspeed and Clover figures are official US-page reads from 2026-10-29; Clover's $16 Starter excludes item/category management and detailed reports, and its online-store fees could not be verified from Clover's own pages.
The Ranking
1. Shopify POS — The Storefront Is the Point
4.0/5 Omnichannel subscore: 5.0
Shopify is the default answer for online + in-store because you're not bolting a register onto a website or a website onto a register — they're the same product. Every plan (from $29/mo annual, $39 monthly) includes the full storefront, POS Lite, one product pool, live two-way stock sync and unified customers. Pickup, local delivery, ship-to-customer and emailed carts are native options, which matters for the mechanics of a hybrid store: web orders show up in the same dashboard where you ring up walk-ins.
Two numbers to plan around: serious retail operations — unlimited staff with roles, returns of any order at any location, counts, purchase orders, low-stock alerts, pro reports — require POS Pro at $89/mo per location (our POS Pro deep-dive review maps every gate), and skipping Shopify Payments costs 0.6–2% per sale depending on plan. Card payments also don't work offline. Neither changes the verdict for this category: nothing else here gives you the same single-system web + store spine.
Pros
- One catalog, live two-way sync, no connector middleman
- BOPIS, local delivery, ship-from-store, email carts native
- Deepest app ecosystem (8,000+) for channel gaps
- Returns of online orders at any register (Pro)
Cons
- POS Pro ($89/location) for real retail workflows
- 0.6–2% extra gateway fee off Shopify Payments
- 100-variant-per-product cap (2,048 rolling out)
- No card payments offline
Choose it if: online and in-store are both real channels now or within your plan for the year. Full Shopify POS review · pricing breakdown · visit Shopify POS →
2. Square — $0 Gets You Both Channels
3.8/5 Omnichannel subscore: 4.0
Square's Free plan is the only genuinely $0 way to run this pair: the register plus a Square Online store, one catalog, pickup and local delivery included on every tier. Rates are flat and readable — 2.6% + 15¢ in person, 3.3% + 30¢ online (2.9% + 30¢ on Plus/Premium), all re-verified from Square's pricing page today, 2026-11-05. The Plus tier ($49 per location) adds what online-and-in-store stores usually need next: inventory tracking, purchase orders, barcode labels, loyalty, custom domain and preorders.
The honest limits: the Square Online storefront is simpler than Shopify's (fewer themes, thinner app depth), stock sync between channels is real but the retail workflows are tier-gated, and Square processing is mandatory. For a store where online is a supporting channel rather than the flagship, that's usually a fine trade — and the cost tables below show exactly where it stops being one.
Pros
- Online store included at $0/mo on every plan
- Flat, published rates on both channels
- Pickup + local delivery included everywhere
- Plus ($49) unlocks inventory, POs, loyalty, custom domain
Cons
- 3.3% + 30¢ online rate on Free is the priciest here
- Storefront depth below Shopify's
- Square processing required
- Transfer orders need Premium ($149)
Choose it if: you want both channels live this week with minimal fixed cost, and your website is “good enough” rather than strategic. Full Square review · visit Square →
3. Lightspeed Retail — Superb Store, Bring Your Own Website
3.6/5 Omnichannel subscore: 3.0
Lightspeed's retail plans ($89/$149/$289 per month on annual billing, verified 2026-10-29) run the deepest in-store operation of the four — matrix variants, serialized stock, purchase orders, receiving, transfers — at 2.6% + 10¢ card-present. The website, however, is a separate decision: the legacy webstore lines are in transition and the practical pattern is pairing Lightspeed with Shopify (an official connector exists) or another platform, which means two subscriptions, two bills and a sync layer between them.
That's a legitimate architecture — Lightspeed for stock operations, Shopify for the storefront — but you should price it honestly: Lightspeed Basic ($89) + Shopify Basic ($29 annual) is $118/mo in software before any processing, and you're paying it for the best back office here, not for the easiest web sync. If online is the bigger half of your business, buy the other way around.
Pros
- Best inventory/PO/receiving engine of the four
- Official Shopify integration for the online half
- 2.6% + 10¢ across all tiers (Lightspeed Payments)
Cons
- No first-party storefront on retail plans today
- Two subscriptions + integration to run and pay for
- eCom line status has changed repeatedly — verify in writing
Choose it if: the back office is the business and you're willing to assemble the web side deliberately. Full Lightspeed review · visit Lightspeed →
4. Clover — Excellent Register, App-Based Online
3.0/5 Omnichannel subscore: 2.5
Clover's counter experience and buy-once hardware are real strengths (official retail bundles, read 2026-10-29: Starter $16/mo × 36 or $349; Retail Growth $84.95/mo with the $1,899 Station Duo or $180/mo × 36). But online selling is App Market territory — including the official BigCommerce integration and third-party Shopify connectors — so catalog sync, order flow and online fees all depend on which app you add, and those figures couldn't be verified from Clover's own pages. One trap to know before pricing it: the $16 Starter tier explicitly excludes item and category management — a hybrid store can't actually run its catalog there.
If you already own Clover hardware for a mostly-walk-in store and want a light web presence, an app path works. Making Clover the spine of a genuinely hybrid business means paying app-by-app for what Shopify includes by default.
Pros
- Best buy-once hardware lineup
- Easy day-to-day register operation
- Official BigCommerce integration; Shopify connectors exist
Cons
- No native online store or sync engine
- Online cost and sync quality unverified (app-dependent)
- $16 Starter excludes catalog/inventory management entirely
- Reseller terms and 36-month contracts
Choose it if: in-store is 90%+ of the business and the web channel can live inside an app. Full Clover review · visit Clover →
What Running Both Channels Actually Costs
Same store, three sizes, one table — every figure computed from the rates above (software on annual billing; Shopify in-person at the published Basic rate, 2.6% + 10¢ — re-read from the official US pricing page 2026-11-05, alongside Shopify's plan-price increase). Assumed average ticket: $40 in-store, $80 online (starter/mid), $50/$100 at scale.
| Setup (monthly cost) | Starter $4k store + $2k web | Mid $8k store + $4k web | Scaled $20k store + $10k web |
|---|---|---|---|
| Shopify Basic + POS Lite | $209 | $388 | $909 |
| Shopify Basic + POS Pro | $298 | $528 | $1,039 |
| Square Free | $193 | $385 | $940 |
| Square Plus | $230 | $410 | $929 |
| Square Premium | — | $502 | $1,009 |
Three findings, and they cut against the marketing on both sides:
- The “free” Square crossover no longer needs a volume argument. At the small $6k/month store, Square Free costs $193 against Shopify Basic + Lite's $209 — before Shopify's late-2026 price increase and published 10¢ per-tap fee, this was a $190-vs-$193 dead heat; now Square Free is cheaper outright at the small and mid sizes ($193/$385 vs $209/$388). Square's remaining online-rate disadvantage (3.3% + 30¢ on Free) is what keeps the mid gap small rather than wide.
- Scale still favors Shopify — but only the Lite half of it. At $30k/month combined, Shopify Lite ($909) is the cheapest full-stack line in the table, edging Square Plus ($929) and Square Free ($940); but add POS Pro and Shopify costs $1,039 — more than Square Plus and Square Premium ($1,009). The old framing (“Pro pays for itself on Shopify's fee edge at scale”) is gone: Shopify's Basic and Plus-adjacent rates now carry the same 10¢ shape as everyone else, and its plan prices went up in late 2026.
- Lightspeed and Clover can't be in this table honestly. Both need a second platform or app for the web half — Lightspeed Basic ($89) plus Shopify Basic ($29) is already $118/mo in software before online fees, and Clover's online-store app pricing is unverified. That two-bills reality is itself the ranking argument.
Methodology and per-fee breakdowns live in our full POS cost guide and processing-fee explainer.
Five Questions to Ask Before You Buy Either Half
- “Does a sale anywhere decrement stock everywhere, and how fast?” Ask for the sync path, not the demo. Manual or scheduled syncs cause overselling on bestsellers.
- “Can a cashier return an online order, and does that need the paid tier?” On Shopify this is a Pro gate; on Square it's included for Retail; on the others it depends on the integration or app.
- “What's my blended rate at my real ticket size?” Percentage-only vs % + fixed flips the winner depending on your transaction count — model it (our cost guide shows how).
- “If online is app/integration territory, who owns it when it breaks?” Connector support contracts are where hybrid-store budgets leak.
- “Can customers buy online, pick up in 20 minutes, and pay nothing extra?” BOPIS mechanics are the cheapest omnichannel win you can get; check they're native, not a workaround.
FAQ
What is the best POS system that handles online and in-store sales together?
Shopify POS, because the storefront and the register are one product — shared catalog, automatic two-way stock sync and native pickup/delivery options. Square is the best low-cost path if an included $0 online store is enough and you don't need Shopify's depth.
Is Square's free online store actually good enough for retail?
For many single stores, yes — the same $0 plan includes the register, Square Online, pickup and local delivery. It falls short on theme/app depth and paid-tier gates: custom domain, preorders and abandoned-cart emails need Plus ($49/mo), and real-time shipping rates need Premium ($149/mo).
Should I run Lightspeed in-store and Shopify online?
It's a common, legitimate pattern with an official connector — but count the cost honestly: two subscriptions ($89 + $29 minimum), two bills, and a sync layer between two vendors' support queues. Choose it for Lightspeed's inventory engine, not for simplicity.
Can Clover sync with my existing Shopify store?
Not natively. Third-party connectors and agencies handle Shopify↔Clover inventory/order sync (BigCommerce's is official). Test the connector with your own catalog — sync quality varies, and Clover's own pages don't publish online-store pricing.
At what point does paying more software save money?
When a free tier's workarounds cost more than the upgrade. In our mid-size model, Square Free ($385) and Shopify Basic + Lite ($388) are effectively tied, but the moment you need purchase orders and stock counts, Square Plus ($410) beats Shopify + Pro ($528) by $118/month — the Lite tier's scale win only holds for stores that can live inside Lite's gates.
How We Ranked These
Final Verdict
Shopify POS is the best POS for selling online and in-store together — one system, one catalog, no connector risk. Square wins if you want both channels live at $0/month and your storefront can stay simple. Lightspeed earns its pairing only from the back-office side, and Clover fits businesses where the website is a supporting player bolted on via apps. Decide which half of your business is the tail wagging the dog, and buy from that end.
Prices and rates checked 2026-11-05 (Square full re-read; Shopify carries its 2026-10-22 USD read after another geo-localised render; Lightspeed and Clover carry 2026-10-29 official reads). Vendors change terms — verify before signing.