Retail Payroll Software: 12 Platforms Compared

If a store owner asked me where to start with payroll, I would say this first: payroll software for a retail store is not the same purchase as payroll software for an office. Here I compare 12 platforms, price the eight that publish rates at 5, 15, and 50 employees, and flag the ones a small store should ignore entirely.

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 look alike, roughly $35 to $50 base plus $5 to $7 per employee, so the choice looks like a coin flip. It is not. Three things decide it: whether hours arrive from your point of sale (POS) or get typed in by hand, whether a second store adds a fee, and whether your plan pays one person at two rates.

What makes retail payroll different

Six characteristics change the requirements, and every one of them is a place where generic payroll advice stops applying.

Turnover drives the rest. Retail runs one of the highest separation rates of any US industry. According to the Bureau of Labor Statistics Job Openings and Labor Turnover Survey, retail workers quit at an average rate of 2.6% a month in 2025, a pace topped only by leisure and hospitality.

High turnover means 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.

12 retail payroll platforms compared

Start with the POS Native column below. It separates products that read hours from your register automatically from products that expect a file or an integration you configure and maintain.

Square Payroll

Square Payroll costs $35 per month plus $6 per person paid, the lowest base fee of any full-service option on the list. 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.

Square includes tax filing across federal and state jurisdictions and free digital W-2 and 1099 delivery, while 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 $49 per month plus $6 per paid employee on top of the location subscription.

Homebase's paid tiers run $30 to $120 per location per month ($24 to $96 on annual billing), and the top All-in-One tier adds onboarding with e-signatures and document storage.

The pricing model is the thing to understand before signing. Homebase's paid plans charge per location with unlimited employees, which is excellent value for one busy store and expensive for three small ones. A second store adds its own location fee even if only four people work there, and the payroll add-on still bills for each person paid.

Gusto

Gusto's Simple plan runs $49 per month plus $6 per employee after a base price increase during 2025, with automatic tax filing, year-end processing, and onboarding and benefits tools built in. For a store owner who wants offer letters, document storage, and health insurance in the same system that runs payroll, Gusto covers more ground than anything else at this price.

Gusto has two retail-specific limitations. Simple is single-state only, so a store across a state line forces Plus at $80 plus $12 per employee. And time tracking sits behind Plus or the Time & Attendance Plus add-on at $6 per person, which means an hourly store on Simple pays extra for its clock and schedules.

OnPay

OnPay sells one payroll plan at $49 per month plus $6 per employee, with no tier to climb and add-ons for time tracking and HR. 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.

The gap for retail specifically is time tracking, which OnPay sells as an add-on at $15 per month plus $4 per worker rather than building it into the base plan. For a store with hourly staff, budget for that add-on or a separate clock.

Patriot Software

Patriot's Full Service plan, at $37 per month plus $5 per employee, is the cheapest full-service payroll in this comparison. It covers federal, state, and local tax filing and deposits, while new hire reporting stays with the employer. The Basic tier at $17 plus $4 calculates tax but leaves depositing and filing to the owner.

Leaving deposits to the owner is a poor trade for a store without a bookkeeper. The IRS sets failure-to-deposit penalties at 2% to 15% of the unpaid deposit, depending on how late it arrives.

Each additional state costs $12 per month. Patriot has no scheduling, and its time clock comes only as a paid add-on. For a single store in one state watching every dollar, nothing on this list beats it on price.

QuickBooks Workforce

QuickBooks Workforce (formerly QuickBooks Payroll) starts with Workforce Payroll at $50 per month plus $7 per employee, following a per-employee price increase across the Workforce plans on July 1, 2026. Federal and state tax filing is included on every tier, while certain local taxes are handled only on Workforce Premium and Elite.

The reason to pick it has always been the same: if the store's books already live in QuickBooks Online, payroll lands in the general ledger with no export step. Time tracking starts on Workforce Premium, which pushes many hourly retailers up a tier, and each additional state adds $12 a month on Workforce Payroll and Premium.

Fingercheck

Fingercheck is built for hourly and deskless teams rather than adapted to them. Its 360 plan lists at $79 per month plus $10 per employee, with a minimum charge equal to five employees.

The plan bundles payroll with Fingercheck's time clock app (facial recognition, plus geofencing that only accepts clock-ins from a set area), scheduling, hiring with candidate screening, and digital onboarding. Multi-state payroll runs in a single pass, but Fingercheck's plan pages do not list tip pooling, so a store that pools tips should confirm how they are handled before buying.

Fingercheck 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

Toast Payroll is the Square equivalent for food service: payroll wired directly into Toast point of sale, with hours flowing from the register and the Tips Manager add-on calculating pooled or shared tips into payroll.

Toast publishes no list price. Each contract bills the higher of a monthly minimum per pay group (a set of employees on the same pay schedule) or a per-employee charge, and some contracts add a base fee.

For a general merchandise or apparel retailer, Toast is the wrong category of product. It is included here because it shows up in retail payroll comparisons despite being a restaurant tool.

Rippling

Rippling builds HR, payroll, and IT around one unified employee record. Its pricing page is a quote form with no published rates. Rippling's small-business page starts payroll at $8 per user a month plus a $40 monthly base fee, and its blog prices the core platform and domestic payroll, a separate module, at $8 per employee a month each on annual billing.

Real configurations land well above those starting figures, because each product is bought on top of the required core platform. Rippling handles multi-jurisdiction tax, and it genuinely scales from a small chain into the mid-market without moving to a new system.

For a single small store 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 case for ADP RUN is its tax service: on every package, ADP calculates, files, deposits, and reconciles payroll taxes and answers inquiries from tax agencies. That service matters for an operator with stores across several states and local tax jurisdictions.

ADP publishes no rates, so all four packages (Essential, Enhanced, Complete, and HR Pro) are priced by quote. No contract is required, and service can be terminated at any time.

Paychex Flex

Paychex Flex is a service relationship rather than a software subscription: the Complete package includes premium support with a payroll specialist, and the Basic, Foundations, and Advanced packages sell that support as an add-on. Every package is priced by request.

The case for Paychex 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.

Paycom

Paycom is a full human capital management (HCM) suite with a retail offering, sold on quote-only pricing that generally starts making sense at enterprise scale. Everything an enterprise retailer needs is present, including learning management, performance, and scheduling in one system.

For the small stores this comparison is written for, Paycom 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.

As headcount grows, the order changes. At 5 employees the base fee does most of the work, and the cheapest and most expensive options in the table differ by $67 per month, a real gap for a small shop.

By 50 employees the per-employee rate takes over: Patriot at $5 and QuickBooks Workforce at $7 end up $113 a month apart, and Fingercheck at $10 costs about twice what Patriot does. So at 5 people, compare base fees, and at 50, compare the per-employee rate, because that number sets most of the bill.

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.

The difference between the second and third rows is manual 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.

Stores on Clover or Lightspeed pair the POS with a separate payroll product, and Lightspeed's own offer is workforce management and payroll powered by Homebase. The quality of any pairing varies by combination.

The multi-location pricing trap

The multi-location pricing trap is the single most expensive misjudgment in retail payroll purchasing. It happens because the pricing model that is cheapest at one store is often the most expensive at three.

Take 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.

The reverse case favors Homebase: one store with 40 hourly staff pays a single location fee that covers scheduling for all of them, though the payroll add-on still bills $6 for each person paid, so the saving sits on the scheduling side.

The state question compounds separately. A second location across a state line means a new registration with the revenue and unemployment agencies of that state before anyone can be paid there, a different minimum wage, and possibly local taxes.

Honest verdict by store size

For one store in one state, start with Patriot, or with Square Payroll if you run Square point of sale. A growing hourly store usually belongs on Homebase, a second store in the same state favors OnPay or Gusto, stores across state lines point to OnPay, and Rippling and Paycom become reasonable from four locations up.

Before you choose

FirstHR is an onboarding and HR platform, not a payroll provider. Payroll runs, wage calculations, and payroll tax filing come from the platforms above, so 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 plans cover it unevenly.

FirstHR covers that layer for small US teams: onboarding workflows that put the I-9 and W-4 on each new hire's first-day task list, e-signatures on offer letters and policy acknowledgments, document storage, training modules with completion tracking, and employee records. It costs a flat $98 a month for up to 10 people or $198 for 11 to 50.

Frequently Asked Questions

What is retail payroll software?

Retail payroll software is 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, October 2026 list rates run $62 for Patriot Full Service, $65 for Square Payroll, $79 for OnPay or Gusto Simple, and $85 for QuickBooks Workforce Payroll. At 50 employees the same plans land between $287 and $400. Fingercheck, which bundles its time clock and scheduling, costs the most at every headcount.

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. Lightspeed sells its merchants workforce management and payroll powered by Homebase, and Clover stores connect a separate payroll provider through 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 adds its own location fee. If the second location is in another state, Patriot and QuickBooks Workforce each add $12 per month, and Gusto Simple requires an upgrade to Plus.

Does retail payroll software handle tips?

It depends on the product. Square captures tips at the register and can pool them, and Toast pools them through its Tips Manager add-on. Homebase sells tip management as a paid add-on. Gusto, OnPay, and Patriot accept reported tips and withhold correctly on them, but none lists pooling as a plan feature. Confirm the mechanics if the store runs a tip pool.

What are fair workweek laws and do they apply to a small store?

Fair workweek laws require covered employers to post schedules roughly 14 days ahead and pay a premium for changes inside that window. Eleven US jurisdictions enforce them, led by Oregon statewide, and most set thresholds of 100 employees or more counted company-wide, so independent stores are usually exempt. New York City, covering retailers with 20 or more employees in the city, is the exception.

Do retail employees with different rates need special payroll software?

Not special software, but a plan supporting multiple pay rates per employee, which Square, OnPay, Patriot, and Homebase all list. Under the federal regular-rate rule, overtime is calculated on a weighted average of the rates worked that week.

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 collecting those forms breaks down: payroll software will pay someone whose new hire paperwork was never finished.