Retail Payroll Software: 12 Platforms Compared
Retail payroll software compared on real cost at 5, 15, and 50 employees, POS integration, multi-location pricing, and scheduling for hourly store teams.
Retail Payroll Software Compared
What each platform costs at 5, 15, and 50 store employees, which ones read hours straight from your register, and the pricing model that punishes a second location
Payroll software for a retail store is not the same purchase as payroll software for an office. An office pays a stable set of salaried people twice a month. A store pays a shifting mix of part-time and full-time staff whose hours change weekly, some of whom hold two different rates, several of whom were hired six weeks ago and will be gone in four months.
That difference is what separates the products below. The pricing pages all look similar, roughly $35 to $50 base plus $5 to $7 per employee, and at first glance the decision looks like a coin flip. It is not. What actually decides it is whether hours arrive from the register automatically or get typed in by hand, whether a second store doubles the subscription or costs nothing extra, and whether the platform handles two pay rates for the same person without an upgrade.
This comparison covers 12 platforms across those criteria, prices each at 5, 15, and 50 employees, and is honest about which ones a 12-person store should ignore entirely.
What makes retail payroll different
Six characteristics change the requirements, and every one of them is a place where generic payroll advice stops applying.
| Characteristic | What it demands from the software | Where products fall short |
|---|---|---|
| Hours vary every week | Time data flowing into payroll without manual entry | Platforms with no built-in time clock require a second subscription |
| Mixed part-time and full-time | Correct overtime on actual hours, accurate PTO accrual | Entry tiers sometimes cap PTO policy complexity |
| Two rates for one person | Multiple pay rates per employee with weighted-average overtime | Often gated behind a higher tier or an add-on |
| Seasonal hiring spikes | Fast onboarding of many people, then pausing without penalty | Per-employee billing on headcount, not on people actually paid |
| Tips and commission | Tip reporting, pooling, and the FICA tip credit | General platforms accept tips as input but do not pool them |
| Multiple locations | One payroll run across stores, states, and local minimum wages | Per-location pricing and per-state surcharges compound quickly |
The turnover point deserves its own paragraph because it drives the rest. Retail runs one of the highest separation rates of any US industry, and the practical consequence is that a store with 15 positions may hire 10 people in a year. Every one of those hires needs tax forms, an I-9, a pay rate in the system, and a first shift they are actually prepared for. Payroll software handles exactly one part of that: paying them correctly once everything else is in place. Our guides to the cost of employee turnover and labor cost cover the numbers behind it.
12 retail payroll platforms compared
The POS Native column below is the one worth reading first. It separates products that read hours from your register automatically from products that expect a file or an integration you configure and maintain.
| Product | Best For | Starting Price | Pricing Model | Tax Filing | Scheduling | POS Native | Onboarding Tools | Trial |
|---|---|---|---|---|---|---|---|---|
| Square Payroll | Stores already on Square POS | $35 + $6/ee | Flat + PEPM | Free trial | ||||
| Homebase | Scheduling first, payroll added | $39 + $6/ee | Per location + PEPM | 14 days | ||||
| Gusto | Depth of HR alongside payroll | $49 + $6/ee | Base + PEPM | Until 1st run | ||||
| OnPay | Multi-state without surcharges | $49 + $6/ee | Base + PEPM | 1 month | ||||
| Patriot | Lowest cost, single location | $37 + $5/ee | Base + PEPM | 30 days | ||||
| QuickBooks | Books already in QuickBooks | $50 + $6.50/ee | Base + PEPM | 30 days | ||||
| Fingercheck | Biometric clock and geofencing | $79 + $10/ee | Base + PEPM | Varies | ||||
| Toast Payroll | Food service on Toast POS | ~$90 + $9/ee | Bundle + PEPM | Demo | ||||
| Rippling | Growing past one system | $35 + $8/ee+ | Modular PEPM | Demo | ||||
| ADP RUN | Compliance depth, multi-location | ~$79 + $4/ee | Quote | 3 months | ||||
| Paychex Flex | A named person to call | Quote | Quote | Varies | ||||
| Paycom | Above 100 employees | Quote | Quote | Demo |
Square Payroll
At $35 per month plus $6 per person paid, this is the cheapest full-service option on the list, and for a store already running Square point of sale the argument is close to unanswerable. Hours, tips, and labor cost flow from the register into payroll with nothing to configure. Tax filing across federal and state jurisdictions is included, digital W-2 and 1099 delivery is free, and paper copies cost $3 per form annually. Contractor-only payroll drops the base fee entirely and charges $6 per contractor paid.
The catch is that most of the value is locked to the Square ecosystem. A store running Clover or Lightspeed gets a competent but unremarkable payroll product with thin HR functionality and basic reporting.
Homebase
Homebase approaches the problem from the scheduling side rather than the payroll side, which for many store operators is the correct order. Drag-and-drop schedules, a time clock, team messaging, and shift trades come first, and payroll attaches as an add-on at $39 per month plus $6 per paid employee on top of the location subscription. Paid tiers run roughly $25 to $100 per month per location, and the higher tier adds onboarding with e-signatures and document storage.
The pricing model is the thing to understand before signing. Homebase charges per location with unlimited employees, which is excellent value for one busy store and expensive for three small ones. A second location is a second full subscription regardless of whether four people work there.
Gusto
The Simple plan runs $49 per month plus $6 per employee after a March 2026 base price increase, with automatic tax filing, year-end processing included, and the best onboarding and benefits tooling among the payroll-first providers. For a store owner who wants offer letters, document storage, and health insurance administration in the same system that runs payroll, Gusto covers more ground than anything else at this price.
Two retail-specific limitations. Simple is single-state only, so one store across a state line forces Plus at $80 plus $12 per employee. And time tracking sits behind Plus or a paid add-on, which means an hourly store on Simple still needs a separate clock.
OnPay
One plan at $49 per month plus $6 per employee with every feature included and no tier to climb. Tax filing covers all 50 states with no multi-state surcharge, which matters for any operator with stores on both sides of a state line. Year-end W-2 and 1099 filing is included and the first month is free without a credit card.
The gap for retail specifically is time tracking, which OnPay does not build in and expects to arrive from an integration. For a store with hourly staff, budget for a clock alongside it.
Patriot Software
Full Service at $37 per month plus $5 per employee is the cheapest legitimate full-service payroll available, covering federal, state, and local filing plus new hire reporting. The Basic tier at $17 plus $4 calculates tax but leaves depositing and filing to the owner, which for a store without a bookkeeper is a poor trade against IRS deposit penalties.
Additional states cost $12 per month each, and there is no scheduling and no built-in time clock beyond a paid add-on. For a single store in one state watching every dollar, nothing beats it on price.
QuickBooks Payroll
Core runs $50 per month plus $6.50 per employee with full-service tax filing on every tier, following a per-employee price increase across the Workforce plans on July 1, 2026. The reason to pick it has always been the same: if the store books already live in QuickBooks Online, payroll lands in the general ledger with no export step. Time tracking arrives on Premium rather than Core, which pushes many hourly retailers up a tier.
Fingercheck
Built for hourly and deskless teams rather than adapted to them. The 360 tier at roughly $79 per month plus $10 per employee bundles payroll, a biometric time clock with geofencing, scheduling, applicant tracking, and an onboarding wizard. Multi-state payroll runs in a single pass and tip pooling is handled natively.
It is meaningfully more expensive per employee than the general platforms, which is the honest trade: you are buying a time and attendance product with payroll attached rather than the reverse.
Toast Payroll
The Square equivalent for food service: payroll wired directly into Toast point of sale, with automatic tip distribution and hours flowing from the register. Pricing is quoted as a bundle with the POS rather than published as a standalone number. For a general merchandise or apparel retailer this is the wrong category of product, and it is included here only because it appears in most retail payroll listicles despite being a restaurant tool.
Rippling
A unified employee record spanning HR, payroll, and IT, starting at $35 per month plus $8 per employee for the core platform with payroll as a separate module. Real configurations land well above the headline figure. Rippling handles multi-jurisdiction tax and connects to Toast, Square, and Lightspeed, and it genuinely scales from a small chain into the mid-market without replatforming.
For a single store with 14 people it is overbuilt and overpriced. The point at which it starts making sense is somewhere north of three locations with real administrative complexity.
ADP RUN
The deepest tax compliance operation in the category, which matters for an operator with stores across several states and local tax jurisdictions. Third-party estimates put the Essential tier near $79 per month plus $4 per employee, but ADP does not publish rates and most buyers report paying more once add-ons land. Contracts typically run annually with automatic renewal.
Paychex Flex
A service relationship rather than a software subscription, with a named contact at higher tiers. Pricing is quote-only. The case for it in retail is specific: when a wage-and-hour question or a tax notice arrives and nobody in the store knows what it means, having someone to call has real value. Customers regularly report quarterly administrative charges not discussed upfront.
Paycom
A full human capital management suite with a retail vertical, sold on quote-based per-employee pricing that generally starts making sense above roughly 100 employees. Everything an enterprise retailer needs is present, including learning management, performance, and scheduling in one system. For the 5 to 50 employee stores this comparison is written for, it is the wrong size of product and the sales process will make that clear.
What retail payroll actually costs at 5, 15, and 50 employees
Vendor pages quote a base fee and a per-employee fee separately, which makes comparison harder than it should be. The table below does the arithmetic at three store sizes and adds the column that reorders everything: what happens at a second location or a second state.
| Product | 5 employees | 15 employees | 50 employees | 2nd Location or State | Notes |
|---|---|---|---|---|---|
| Patriot Full Service | $62 | $112 | $287 | $12/mo per extra state | No scheduling included |
| Square Payroll | $65 | $125 | $335 | Included | Needs Square POS to shine |
| Homebase + payroll | $94 | $154 | $364 | Per location, not state | Second store roughly doubles base |
| OnPay | $79 | $139 | $349 | Included | No built-in time clock |
| Gusto Simple | $79 | $139 | $349 | Forces Plus tier | Plus at 15 staff is $260 |
| QuickBooks Core | $83 | $148 | $375 | Fee per extra state | Time tracking on Premium |
| Fingercheck 360 | $129 | $229 | $579 | Included | Biometric clock included |
The pattern worth naming is that the spread narrows as headcount grows. At 5 employees the cheapest and most expensive SMB options differ by $67 per month, a real gap for a small shop. At 50 employees the general platforms cluster between $287 and $375, a difference of under $90 across very different products. Which means at 50 people the decision should be made on capability rather than price, and at 5 people price is a legitimate deciding factor. For a wider view across the whole payroll category rather than retail specifically, see the payroll software for small business comparison.
POS integration and where it actually breaks
Every vendor lists point of sale integrations. The listing tells you almost nothing, because three different things travel under that word.
| Integration type | What happens each pay period | Products |
|---|---|---|
| Native | Hours and tips are already in payroll: nothing to do | Square with Square POS, Toast with Toast POS |
| Automatic sync | A connector pushes hours on a schedule: verify and approve | Homebase, Gusto, OnPay, Rippling with major POS systems |
| File export | Download from the POS, format, upload to payroll | Various combinations, especially older or niche POS systems |
The difference between the second and third rows is 20 to 40 minutes of work every pay period plus a recurring opportunity for transcription errors. Before buying, ask the vendor specifically whether your point of sale syncs automatically or exports a file, because both answers get marketed as an integration. Clover and Lightspeed in particular do not sell payroll of their own, so store operators on those systems are always pairing a POS with a third-party payroll product and the quality of that pairing varies by combination.
The multi-location pricing trap
This is the single most expensive misjudgment in retail payroll purchasing, and it happens because the pricing model that is cheapest at one store is often the most expensive at three.
| Pricing model | Cost of a second store | Products | Best when |
|---|---|---|---|
| Per employee | Nothing extra: fee follows headcount | Gusto, OnPay, Square, Patriot, QuickBooks | Several small stores |
| Per location | A second full subscription regardless of size | Homebase | One store with many staff |
| Per state | A surcharge on top of either model | Patriot at $12, QuickBooks on some tiers | Everything in one state |
| Tier upgrade | Forces a higher plan entirely | Gusto Simple to Plus | Single state, no expansion planned |
Work an example. Three small stores with six people each, all in one state. On a per-employee platform that is 18 employees and one subscription. On Homebase it is three location subscriptions plus the payroll add-on, and the scheduling value that justified the choice at one store is now being paid for three times. Reverse it: one store with 40 hourly staff on a per-location plan carries unlimited employees for a flat fee, which the per-employee platforms cannot match.
The state question compounds separately. A second location across a state line means a new registration with that state's revenue and unemployment agencies before anyone can be paid there, a different minimum wage, and possibly local taxes. Our multi-state payroll guide covers the mechanics and payroll taxes by state covers what changes where.
Honest verdict by store size
Before you choose
FirstHR does not run payroll, calculate wages, or file payroll taxes. Every platform above does something we do not, and if paying your staff correctly is the problem in front of you, one of them is the answer.
What we handle is the part that happens before the first paycheck. A store that hires 10 people a year and doubles headcount for the holidays is collecting W-4s and I-9s under time pressure, chasing signatures, and hoping each new hire is trained enough to work a shift alone. That is onboarding, and payroll software touches almost none of it. FirstHR covers e-signatures, document collection, training modules with completion tracking, task workflows, and employee records for US teams of 5 to 50 people at a flat $98 to $198 per month, alongside whichever payroll platform you pick.
Frequently Asked Questions
What is retail payroll software?
Payroll built for an hourly, shift-based workforce rather than a salaried one. It reads clocked hours instead of assuming a fixed salary, handles a mix of part-time and full-time staff with different rates, calculates overtime on actual hours under FLSA rules, and often handles tips and commission. Most options are general small business payroll platforms with the retail-relevant pieces turned on.
How much does payroll software cost for a retail store?
At 5 employees, published July 2026 rates run roughly $62 for Patriot Full Service, $65 for Square Payroll, $79 for OnPay or Gusto Simple, and $83 for QuickBooks Core. At 50 employees the same plans land between $287 and $375. Platforms bundling scheduling and time tracking cost more at every headcount because they replace a second subscription.
Which payroll software integrates with Square, Clover, or Lightspeed?
Square Payroll is native to Square and Toast Payroll is native to Toast, meaning hours and tips arrive without configuration. Clover and Lightspeed do not sell payroll of their own, so stores on those systems pair a third-party payroll product with an integration. Confirm whether a given pairing syncs automatically or only exports a file you upload manually.
How does multi-location retail change payroll pricing?
Per-employee platforms including Gusto, OnPay, Square, and Patriot charge nothing extra for a second store. Homebase prices per location, so each store is a separate subscription. If the second location is in another state, Patriot adds $12 per month, QuickBooks may charge per state, and Gusto Simple requires an upgrade to Plus.
Does retail payroll software handle tips?
Square and Toast handle tips natively including pooled distribution, since they capture them at the register. Homebase sells tip management as a paid add-on. Gusto, OnPay, and Patriot accept reported tips and withhold correctly on them but do not pool or distribute tips. Confirm the mechanics if the store runs a tip pool.
What are fair workweek laws and do they apply to a small store?
They require covered employers to post schedules roughly 14 days ahead and pay a premium for changes inside that window. Eleven US jurisdictions enforce them as of 2026, led by Oregon statewide. Coverage thresholds are usually counted globally and set in the hundreds of employees, so most independent stores are exempt. Berkeley at 10 employees is the notable exception.
Do retail employees with different rates need special payroll software?
Not special software, but a platform supporting multiple pay rates per employee, which some gate behind a higher tier. Overtime must be calculated on a weighted average of hours worked at each rate. See our guide to salary versus hourly pay for how the classifications differ.
What payroll work stays with the store owner after setup?
Worker classification, registering in each new state, keeping the unemployment rate current, reviewing quarterly returns, and collecting a complete W-4 and I-9 from every hire before their first shift. Seasonal hiring is where that last one breaks down: payroll software will pay someone whose new hire paperwork was never finished.