OnPay vs Paychex Flex

Whether your business has 10 employees or 100, finding the right payroll provider to meet your needs is essential. Ultimately, they should help in getting your team paid accurately and efficiently, no matter what stage your business is in.


While both OnPay and Paychex Flex have similar capabilities in terms of full-service payroll, HR, and benefits administration, one may be a better fit for you depending on what you’re looking for. So, here are the details about both OnPay and Paychex Flex to help you make a more informed decision.

Whether your business has 10 employees or 100, finding the right payroll provider to meet your needs is essential. Ultimately, they should help in getting your team paid accurately and efficiently, no matter what stage your business is in.

Jump to compare OnPay and Paychex Flex by:

Ratings and Reviews | Pricing and Features | Support

Compare ratings and reviews

We’ve collected reviews from both OnPay and Paychex Flex clients as well as industry experts. Take a look at how small businesses and experts compare Paychex Flex and OnPay:

Customer ratings Expert reviews

OnPay

Paychex Flex

Ease of Setup

92%
84%

Ease of Admin

96%
87%

Quality of Support

97%
86%

Performance

99%
88%

Reliability

98%
89%

Customization

94%
77%

Reporting

98%
86%

Based on G2Crowd ratings

OnPay

Ease of Setup

92%

Ease of Admin

96%

Quality of Support

97%

Performance

99%

Reliability

98%

Customization

94%

Reporting

98%

Paychex Flex

Ease of Setup

84%

Ease of Admin

87%

Quality of Support

86%

Performance

88%

Reliability

89%

Customization

77%

Reporting

86%
Try OnPay's top-rated payroll

Compare features and pricing

We know there’s a lot to consider when choosing your payroll solution, and it’s important you choose a provider that meets both your business needs and your budget. To help spot differences between the two, here’s how OnPay stacks up against Paychex when it comes to specific features and pricing:

OnPay Paychex Flex
Pricing
Base price $36 per month No published price.
Negotiate with sales.
Price is per pay run, not monthly
Per worker cost $4 per person.
Only pay for active workers paid that month.
No published price.
Negotiate with sales.
Price is per pay run, not monthly.
Full-service payroll
Automated federal, state, and local tax filings and payments Included Included
Unlimited pay runs Included Additional fees
Multi-state payroll Included Additional fees
Edit or cancel a pay run Included Additional fees
Multiple pay rates and schedules Included Included
Garnishments Included Included
Accounting and time tracking integrations Included Time tracking integration: Included
Accounting integration: Additional fees
New hire reporting Included Included
Year-end filings, W-2s, and 1099s Included Additional fees
Onboarding and Employee Self-Service
Employee self-onboarding Included Additional fees
Employee self-service portal Included Included
Document e-sign for I-9s and W-4s Included Additional fees
Send and sign offer letters electronically Included Not available
Employee lifetime account access Included Not available
HR and Team Management
Manage and track time off Included Included
Org charts Included Additional fees
Document storage and audits Included Additional fees
Custom onboarding workflows Included Additional fees
Benefits and Compliance
Medical, dental, and vision plans Pay premiums only Additional fees
Integrated workers’ comp plans Pay premiums only Additional fees
Integrated 401(k) plan Pay premiums only Additional fees
Reporting and Usability
Payroll and employee reports Included Included
Real-time reporting filters Included Not available
Custom report designer Included Additional fees

Compare support

Choosing the most reliable payroll service is important, but you’ll also want to be sure your provider will be there to answer your questions and help get past any speed bumps you may face along the way. Here’s how customer support compares between OnPay and Paychex Flex:

OnPay Paychex Flex
Setup and data migration Included Additional fees
Expert phone support Included Included
Chat support Included Included
Accuracy guarantee Included Not available

Decide what payroll features you need

Every small business has different needs, so make sure you know exactly what you’ll be getting. Most notably, take a closer look to understand everything Paychex Flex and OnPay do to simplify paying and managing your team. And if you need to go above and beyond payroll, make sure you understand how much HR, benefits, and integrations with accounting software will all cost so there are no surprises later.


Full-service payroll: Not only do you want a platform to be able to pay your team quickly and easily, but you also want to be sure that your payroll provider will get your local, state, and federal taxes filed and paid accurately, so you can rest knowing things are done right. If you have employees in multiple states or locations, consider whether your provider will charge an additional fee.


With OnPay’s accuracy guarantee, you can be sure your taxes are being filed and paid correctly, no matter how many states your workers are located in — at no additional cost. Note that Paychex Flex charges extra fees for multi-state payroll.



Integrations: Great payroll providers will also have integrations with time-tracking and accounting software. In a perfect world, you want your time and attendance system to talk to your payroll system and in turn, have those expenses flow right to your accounting platform.


OnPay integrates with top accounting and time-tracking systems at no extra cost. Our flexible integrations with QuickBooks and Xero give you the ability to customize data and view your finances in the way that makes the most sense for your business.



Specialized payroll requirements: Businesses in different industries (and of different sizes) sometimes have different payroll tax and withholding requirements. From filing Form 943 filing for ag businesses to accurately processing special pay types like bonuses, tips, or commissions, take a close look to ensure all your needs will be met.


OnPay serves businesses from all industries including farms and ranches, construction, restaurants, doctors, nonprofits, start-ups, and more. So, we can handle any specialized payroll requirements for your business, at no additional cost.



HR and compliance: The best payroll providers will not only help you with payroll, but also with HR and compliance through features like employee self-service, PTO tracking and approval, e-signable documents and storage, organization charts, and more. And, they should also offer integrated benefits and workers’ comp plans (without extra fees for the features and integrations you’ll need).


OnPay offers a full suite of HR tools to help you take care of your team ⁠— at no extra cost. And with integrated pay-as-you-go workers’ comp and benefits plans in all 50 states, we’ll make sure you’re staying compliant while keeping your employees happy.



Account setup and customer support: When getting set up with a payroll provider, it can feel like a long and complex process to get all your data migrated. That’s why your payroll provider should offer to migrate all your prior wage and employee data for free, including help getting all your integrations set up. This level of service makes for a much more seamless transition. You also want to know that your payroll provider will be there to help beyond just setup, in case you have questions or need help with anything in the future.


OnPay will set up your account and migrate all your prior wage and employee data for free, so setup is simple. Note that Paychex Flex charges an additional setup fee. And, with OnPay, you can get help from a payroll expert whenever you need it. Email support begins at 7 AM EST on weekdays, while phone and chat are available from 9 AM to 8 PM EST.



At first glance, both Paychex Flex and OnPay have similar features and functionality, but OnPay consistently receives better ratings and reviews from clients and industry experts alike. See why for yourself:

See how OnPay delivers a higher level of service

We’ll even migrate all your employee info and prior wages for you.

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