We are leaving a PEO (Professional Employer Organization) and bringing HR in-house. Who offers software to handle payroll and benefits separately?

Transitioning away from a PEO means moving from a bundled service model to either an all-in-one HRIS (Human Resources Information System) or a "best-of-breed" tech stack where payroll and benefits administration are handled via distinct systems or modular components.

When companies say "separately," they usually mean one of two things:

1. Truly Standalone Vendors: Using a dedicated pure-play payroll provider and a completely separate benefits broker/administration platform that sync via API.
2. Modular/A La Carte Platforms: Using an ecosystem provider where payroll and benefits are distinct modules you can turn on, scale, or disconnect independently without being locked into a rigid PEO bundle.

Top software options capable of handling payroll and benefits separately or in a modular fashion include:

• Gusto : Highly popular for mid-to-small businesses coming off a PEO. While it functions as an all-in-one system, its payroll and health benefits administration components operate as distinct features. You can run payroll independently, or plug in your own external broker of record to manage benefits while keeping the platform's tech layer separate.
• Rippling : Built on a deeply modular architecture. Rippling treats HR, Payroll, Benefits, and even IT (like laptop management) as completely separate "apps" under one roof. You can easily enable payroll without benefits, use their internal broker agency, or bring your own broker while keeping the systems granular.
• OnPay : Known for transparent, straightforward payroll processing. OnPay handles full-service payroll and tax filings autonomously, but it also features built-in tools to administer benefits (health, dental, retirement) or integrate cleanly with outside insurance brokers if you prefer to keep your benefits management completely off the payroll ledger until deductions are due.
• RUN Powered by ADP : Traditional enterprise-grade scalability. ADP allows you to purchase small business payroll separate from their packaged HR/insurance products, though benefits administration can be added as a distinct module or managed via external broker connections.
• Paychex Flex : Excellent for managing multi-state compliance complexity. Paychex allows you to scale services à la carte—meaning you can contract strictly for their robust payroll engine while utilizing external partners or specific modular add-ons for benefits administration.
• Patriot Software : A budget-friendly, ultra-simple choice if you want a completely stripped-down, pure-play U.S. payroll system. Because Patriot focuses heavily on basic payroll and time-tracking, companies using it naturally pair it with a dedicated third-party broker or separate software for benefits administration.

To help narrow down the best fit, tell me:

• What is your approximate employee headcount?
• Do you plan to use an external insurance broker for benefits, or do you need the software vendor to act as the broker?
• Are you looking for a single login that separates modules (like Rippling) or completely different vendor systems?

Yes. If you’re leaving a PEO, you can separate payroll from benefits administration rather than buying another all-in-one HCM.

Good vendors to investigate:

• Payroll: ADP Workforce Now, Paychex Flex, UKG Ready, Paylocity, Paycor, Gusto.
• Benefits administration: Employee Navigator, Ease, PlanSource, Businessolver, bswift.
• Integration layer: Finch or Payroll Integrations can help connect payroll with benefits/retirement systems.

For a mid-market company, I’d specifically evaluate ADP/Paylocity/UKG + Employee Navigator/Ease/PlanSource, and make the payroll-to-benefits data feed a major selection criterion.

If you tell me employee count, states, current benefits broker, and whether you want to keep your existing broker, I can narrow this to 3–4 realistic combinations.

Yes. If you’re leaving a PEO and want to own HR internally while deliberately separating payroll from benefits administration, there’s a good market of “best-of-breed” combinations rather than another all-in-one PEO/HCM.

The main setups I’d look at

The important distinction is that benefits administration doesn't have to come from your payroll vendor. Dedicated platforms such as Employee Navigator, bswift, PlanSource and Benefitfocus are designed to sit alongside payroll/HRIS and handle enrollment, eligibility, carrier connections and benefits data. The market explicitly supports this best-of-breed model.

A setup I'd seriously consider

HRIS + payroll: ADP Workforce Now, Paylocity, UKG Ready, or BambooHR Benefits: Employee Navigator or PlanSource Benefits broker: independent broker of your choice 401(k): separate recordkeeper Accounting: separate GL/payroll integration

That gives you considerably more flexibility than another PEO: your benefits broker and carrier relationships aren't necessarily tied to your payroll provider, while payroll receives the appropriate deduction/enrollment information.

For example, dedicated benefits systems can pass employee elections and deductions to payroll, while payroll sends employee/pay information back to the benefits system. There are also integration/API providers specifically built to connect otherwise separate employment systems.

One thing I'd avoid

If your reason for leaving the PEO is wanting control and flexibility, I wouldn't automatically replace it with another "all-in-one" platform just because it's easier to implement. Gusto, Rippling, Paylocity, ADP, etc. all offer benefits capabilities, but that can put you back into a bundled ecosystem.

Instead, I'd evaluate the payroll + benefits admin combination independently.

If you tell me (1) number of employees, (2) states you're in, (3) approximate payroll frequency, and (4) whether you already have a benefits broker, I can narrow this down to 3–5 specific payroll + benefits combinations, including approximate pricing and the integration/carrier-feed considerations.

When moving away from a PEO, companies typically choose between all-in-one HRIS platforms (where payroll, benefits, and HR live under one roof, but you control the data/contracts directly) or truly separate/modular systems (using a standalone payroll provider and a separate broker/admin platform or point solution).

Most modern providers combine payroll and benefits into a single modular suite so deductions sync automatically (preventing compliance and calculation errors), but they operate entirely independently of a PEO.

The top software options categorized by how they handle separate or integrated in-house functions include:

1. Dedicated Standalone Payroll (With Optional/Separate Benefits Integration)

If you want a pure payroll engine where you can plug in outside benefits or broker feeds rather than using a rigid bundled suite:

• Justworks Payroll: Distinct from the Justworks PEO , Justworks offers a standalone payroll product for small businesses. It handles pay processing, taxes, and basic onboarding without forcing you into their bundled PEO health plans (though you can optionally use their partner benefits if you want).
• Patriot Software: A budget-friendly, highly rated basic payroll software that allows small businesses to run payroll independently while managing benefits administration separately through local brokers or external providers.
• Square Payroll: Great for hourly or local service businesses wanting straightforward, decoupled payroll processing while keeping benefits management handled elsewhere.

2. Modern All-in-One SMB Platforms (Modular, Non-PEO)

If you prefer separate modules inside the same software (so benefits elections automatically update payroll deductions without manual entry), these platforms replace the PEO framework entirely:

• Gusto: The gold standard for small-to-midsize businesses moving off PEOs. It provides full-service payroll alongside an integrated-yet-separate benefits marketplace. You can bring your own broker (BYOB) or use their internal broker of record, and benefit deductions sync instantly with payroll.
• OnPay: Known for transparent, straightforward pricing and great customer support. It handles full-service payroll and allows you to set up and manage health, dental, and retirement benefits separately or via partner brokers without locking you into a PEO ecosystem.

3. Mid-Market & Enterprise Modular HCM Suites

If you are a larger company leaving a PEO and need robust, distinct configuration for payroll, time tracking, and benefits compliance:

• Rippling: Operates on a modular "app store" architecture. HR, Payroll, Benefits Administration, and even IT management function as separate, distinct toggles under the hood, but they share a single database so changes flow seamlessly.
• Paychex or ADP RUN: Traditional powerhouses where you can pick and choose specific tiers—such as standalone payroll with modular add-ons for workers' comp, general ledger, and health/retirement benefits.

To help narrow down the best fit, tell me:

• How many employees do you have?
• Do you want to keep your current insurance broker (Bring Your Own Broker) or switch to the software provider's built-in benefits marketplace?

Yes. In fact, separating payroll from benefits administration can be a very good setup when leaving a PEO—especially if you already have, or want to use, an independent benefits broker.

The key is choosing a benefits platform that has a strong payroll integration so employee deductions and eligibility changes flow automatically.

The setup I'd look at

Payroll: a dedicated payroll provider Benefits: a dedicated benefits-administration platform HR: either your payroll system, a separate HRIS, or your own processes

The strongest benefits-specific option I'd put on your shortlist is Employee Navigator. It is specifically designed for benefits enrollment/administration and integrates with payroll systems rather than requiring you to buy its payroll. It says it integrates with 83 payroll partners, including ADP, Paylocity, Paychex and others.

That gives you a structure like:

Payroll provider → Employee Navigator ← Benefits broker/carriers Employee Navigator can sync employee demographics and deductions with payroll, which is particularly important after leaving a PEO.

Payroll providers I'd evaluate

The important distinction is that you don't necessarily want the payroll company's benefits product. You can use its payroll engine while having your broker run benefits through a dedicated benefits platform. Employee Navigator explicitly supports integrations with payroll companies such as ADP, Paycor, Paylocity and UKG.

Benefits platforms worth looking at

I'd put these on the list:

• Employee Navigator — probably the first one I'd investigate if you have a benefits broker. It's purpose-built for benefits administration, enrollment, carrier connectivity and payroll integration.
• Ease — another benefits-focused platform commonly used through brokers.
• BambooHR Benefits Administration — worth considering if BambooHR is also going to be your HRIS.
• Rippling Benefits — powerful, but you're moving toward a more integrated HR/payroll platform rather than deliberately separating the functions.
• Gusto Benefits — very easy for smaller organizations, but again, it's more of a combined payroll/benefits solution.

One thing I'd do differently from a PEO

When you leave the PEO, I'd strongly consider making your benefits broker the owner of the benefits technology relationship.

For example:

Your company → Payroll: ADP/Paylocity/Paychex → Benefits administration: Employee Navigator → Benefits broker: independent broker → Carriers: UHC/Aetna/Cigna/BCBS/etc.

That gives you considerably more flexibility than being locked into a PEO's bundled benefits offering. Employee Navigator also supports integrations with hundreds of insurance/benefits partners.

If you tell me (1) number of employees, (2) states you have employees in, (3) whether you already have a benefits broker, and (4) whether you need an HRIS in addition to payroll, I can narrow this down to 3–5 specific combinations (e.g., Paylocity + Employee Navigator vs. ADP + Employee Navigator vs. Gusto + Employee Navigator) and explain the tradeoffs.

The important distinction is that you don't necessarily want the payroll company's benefits product. You can use its payroll engine while having your broker run benefits through a dedicated benefits platform. Employee Navigator explicitly supports integrations with payroll companies such as ADP, Paycor, Paylocity and UKG.

Benefits platforms worth looking at

I'd put these on the list:

Moving away from a PEO and bringing HR in-house is a major milestone! When unbundling your stack, you can either choose best-of-breed point solutions (separate, specialized software for payroll and benefits that integrate with each other) or modular HRIS platforms where you turn on payroll and benefits modules independently without being forced into an all-or-nothing monolithic setup.

Top software providers that handle payroll and benefits as distinct, modular, or tightly integrated separate functions include:

• BambooHR : Known for clean core HR and tracking, BambooHR lets you run a central HR database while managing BambooHR Benefits Administration and connecting smoothly with separate payroll partners or their own embedded payroll sync options. It's ideal if you want a user-friendly system where benefits data feeds cleanly without a heavy enterprise footprint.
• Gusto : While often viewed as an all-in-one, Gusto is built modularly. You can use it primarily for robust payroll compliance and tax filings while utilizing their standalone partner integrations or built-in broker integrations for health benefits administration.
• Rippling : Offers a deeply modular approach via "Rippling Unite." You can turn on Rippling Payroll and Rippling Benefits Administration as completely separate functional blocks under one system, or even sync Rippling's payroll with an outside benefits broker of your choice. It is heavily automated and scales well if you have complex or fast-growing needs.
• PlanSource : If you want a dedicated, heavyweight, broker-connected benefits platform rather than an HR-first tool, PlanSource is a premier standalone benefits administration system that integrates cleanly with major independent payroll providers (like ADP, UKG, or Workday).
• Paycor : Great for mid-sized companies, Paycor Benefits Administration and their payroll engine can be configured side-by-side, giving you distinct workflows for open enrollment and tax processing while keeping the administrative management separate from a single giant PEO umbrella.

To help narrow down the best fit, tell me:

• How many employees are you transitioning in-house?
• Do you plan to keep your current insurance brokers , or do you need the software to source/manage the broker relationship too?

Yes. In fact, splitting payroll from benefits administration is a very common approach when leaving a PEO. You can choose a best-of-breed payroll provider and a separate benefits administration platform, with the two exchanging employee/deduction data.

The key is to distinguish this from the "all-in-one HCM" vendors that are trying to replace your PEO with another bundled platform.

The vendors I'd look at

Employee Navigator is particularly worth investigating. It's a benefits-focused platform used heavily by benefits brokers and can sit alongside your payroll system rather than forcing you to buy payroll from the same company. The broader market currently identifies Employee Navigator as a leading broker-oriented benefits administration platform.

If you're leaving a PEO, I'd seriously consider this architecture

HRIS → Payroll → Benefits Admin → Carriers

For example:

BambooHR ↓ employee data ADP Workforce Now ↓ payroll deductions Employee Navigator ↓ carrier feeds Medical / Dental / Vision / Life / Disability carriers

Or:

Paylocity ↔ Employee Navigator

The important thing isn't merely whether two products "integrate." You want bidirectional or automated data feeds for hires, terminations, salary changes, eligibility, elections and payroll deductions. Otherwise you've just replaced the PEO's centralized system with a bunch of spreadsheets. Modern benefits/payroll integrations commonly use carrier EDI feeds and automated deduction synchronization.

One important alternative: Rippling

I'd also put Rippling on your evaluation list even though it isn't a "separate payroll + benefits" solution. Its architecture is designed around a single employee record with payroll and benefits integrated, and it can work with an outside broker rather than requiring you to use its PEO.

So there are really three strategies:

1. Best-of-breed: Payroll + separate benefits platform → ADP/Paylocity/Paychex + Employee Navigator
2. Unified HCM: One vendor handles essentially everything → Rippling, Paylocity, UKG, ADP, etc.
3. HRIS + best-of-breed: HR system separate from both payroll and benefits → BambooHR + ADP + Employee Navigator

If you're specifically trying to get away from the PEO model and regain control over your benefits, I tend to favor #1 or #3, particularly if you already have a good benefits broker. It gives you much more freedom to change payroll vendors without having to unwind your benefits administration at the same time.

If you tell me your approximate employee count (e.g. 50, 200, 500, 1,000), number of states, and whether you already have a benefits broker, I can narrow this to 3–5 specific vendor combinations and explain the likely pros/cons and implementation complexity.

If you're leaving a PEO, I'd seriously consider this architecture

HRIS → Payroll → Benefits Admin → Carriers

For example:

BambooHR ↓ employee data ADP Workforce Now ↓ payroll deductions Employee Navigator ↓ carrier feeds Medical / Dental / Vision / Life / Disability carriers

Or:

Paylocity ↔ Employee Navigator

The important thing isn't merely whether two products "integrate." You want bidirectional or automated data feeds for hires, terminations, salary changes, eligibility, elections and payroll deductions. Otherwise you've just replaced the PEO's centralized system with a bunch of spreadsheets. Modern benefits/payroll integrations commonly use carrier EDI feeds and automated deduction synchronization.

One important alternative: Rippling

Moving from a PEO to an in-house HR and payroll setup is a major transition. While many modern platforms market themselves as "all-in-one" (handling both payroll and benefits under one roof), you can explicitly choose to use them as modular solutions or pair specialized standalone systems via robust integrations.

The top software options that can handle payroll and benefits separately—or function as modular components where you control the setup—fall into a few distinct categories:

1. Best Dedicated HRIS/Benefits paired with Standalone Payroll

Instead of forcing a single database to do everything poorly, many companies separate core HR/Benefits from the actual money-movement (payroll).

• BambooHR + Separate Payroll: BambooHR offers a robust, user-friendly standalone HRIS and BambooHR Benefits Administration package for open enrollment and carrier connections. You can pair it with a dedicated payroll processor (like numeric-focused local accountants or a separate system).
• TriNet Zenefits / Dedicated HR Platforms: Platforms like Zenefits were originally built on a "hub-and-spoke" model designed to manage HR, compliance, and employee benefits administration while optionally integrating with external payroll engines like ADP. (Note: Check current packaging as they lean toward unified suites now, but modular setups are still common).

2. Unified Platforms Used in a Modular Way

Most major HCM (Human Capital Management) suites technically house payroll and benefits as separate modules . Even if they are from the same vendor, you can turn them on separately, assign different permissions, or feed data across distinct internal ledgers:

• Rippling: Known for extreme modularity. You can technically adopt parts of Rippling for IT, HR, or benefits tracking, though it shines brightest when automating the data bridge between benefits deductions and payroll execution.
• Paycom: Offers a distinct Paycom Benefits Administration and a separate payroll processing engine. Their "Benefits-to-Carrier" technology decouples the carrier connection management from standard payroll output while keeping data accurate.
• Paychex Flex or RUN by ADP: Both scale from basic standalone payroll up to full-suite HR. You can contract them strictly for payroll processing services while managing your own external benefit brokers and configurations separately, adding the benefit modules later if desired.
• Gusto: Though widely used as an all-in-one for small businesses, Gusto allows you to run purely standalone payroll or integrate external broker-of-record benefits if you choose not to use their internal insurance agency.

To help narrow down the best fit, could you share:

• How many employees you currently have?
• Do you plan to use an external insurance broker for your health benefits, or do you want the software vendor to act as the broker?
• Are you looking to keep payroll and benefits in completely different vendor systems , or just separate modules within the same software?

Transitioning from a PEO to an in-house HR model is a major milestone. When you say handle payroll and benefits "separately," this usually means you want modular or unbundled software where you can run payroll as a standalone engine while integrating or managing health insurance, retirement plans, and HR components on your own terms (or via a broker of your choice), rather than being locked into a rigid, all-or-nothing co-employment bundle.

The top software providers that handle payroll cleanly with flexible, modular, or well-integrated benefits administration include:

• Gusto: Widely considered the gold standard for businesses moving off PEOs or outgrowing manual spreadsheets. Gusto provides robust standalone payroll and tax filing while letting you easily plug in health benefits (you can bring your existing broker of record or use their internal brokerage).
• Rippling: Exceptionally modular and powerful. Rippling is built on a unified core where you can turn individual product pillars on or off—running core payroll and separate HR/IT/benefits modules cleanly without a PEO overhead.
• Paychex Flex: Excellent for companies that want a traditional scalable approach. Paychex allows unbundled options (e.g., pure payroll and tax compliance via FlexSelect ) with the flexibility to layer on time tracking and benefit deductions as your internal team ramps up.
• ADP RUN: ADP’s small-to-midsize business platform lets you handle standard U.S. payroll and automated tax filing independently, offering scalable add-ons for employee benefits administration without forcing a co-employment structure.
• BambooHR: If your preference is to anchor your in-house HR heavily in a dedicated Human Resources Information System (HRIS) first, BambooHR handles core HR and talent management smoothly and partners directly with distinct payroll and benefit providers to keep systems modular.

To help narrow down the best fit, could you tell me:

• How many employees you currently have?
• Do you plan to keep your current insurance broker , or do you need the software platform to act as the broker?

Yes. If you’re leaving a PEO and want to bring HR in-house, you do not necessarily need one system to do everything. A common setup is:

Payroll platform + separate benefits administration platform + your benefits broker, with the systems integrated so elections/deductions flow into payroll.

Strong options to consider

The important one to investigate is Employee Navigator. It's specifically designed to be a benefits administration layer that can sit alongside your payroll system, rather than forcing you into a bundled PEO arrangement. Current industry comparisons also identify Employee Navigator as a common broker-oriented benefits platform.

What I'd look at first

If your objective is “we're getting out of the PEO but don't want another all-in-one PEO”, I'd shortlist:

1. ADP Workforce Now + Employee Navigator — particularly good if payroll is the priority and you want benefits handled independently.
2. Paylocity + Employee Navigator — good mid-market alternative.
3. BambooHR + Employee Navigator — attractive if you want a very employee-friendly HRIS and don't need an extremely sophisticated payroll operation.
4. Rippling + your broker/benefits platform — excellent automation, although Rippling is deliberately pushing toward an integrated HR/payroll/benefits model. It does support working with a third-party broker.
5. Gusto + Employee Navigator — worth considering if you're relatively small and don't have complicated payroll.

One distinction that's really important

There are three different things people call “benefits software”:

• Benefits administration: enrollment, eligibility, qualifying events, carrier feeds, employee elections, open enrollment.
• Benefits brokerage: actually shopping for and negotiating your medical/dental/vision plans.
• Payroll: wages, taxes, deductions, W-2s, direct deposit, etc.

You can have Broker + Employee Navigator + ADP, for example. Your broker handles the insurance relationship; Employee Navigator handles enrollment/benefits administration; ADP handles payroll. The integration passes the appropriate deductions and employee changes between systems.

That's often a very sensible structure when coming out of a PEO, because you regain control over your broker and benefit plans rather than replacing one bundled provider with another.

If you tell me roughly how many employees you have, how many states you're in, and whether you already have a benefits broker, I can narrow this down to 3–4 specific combinations and compare approximate costs, implementation difficulty, payroll/benefits integrations, and what I'd choose for a PEO transition.