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Paychex Flex for Small Non-profit Payroll Administration
Updated April 25, 2023

Paychex Flex for Small Non-profit Payroll Administration

Lonnie deMarco | TrustRadius Reviewer
Score 8 out of 10
Vetted Review
Verified User

Overall Satisfaction with Paychex Flex

I administer Paychex Flex for payroll on behalf of one of my non-profit clients. This client had implemented Paychex Flex in 2019 to enhance their payroll administration to include both Full-time and part-time employees, as well as 1099 contract workers. Paychex flex offered my client an opportunity to reduce their overall business cost by switching payroll providers while providing a more user-friendly web portal and increased helpdesk support.
  • Ease of admin interface and use for non-HR professionals.
  • Accurate calculation of appropriate payroll taxes.
  • Ability for payroll admin to make changes/corrections to standard payroll run.
  • Accurate setup of pre-tax deductions.
  • Long hold time for helpdesk (may be covid-related - this has been much better in the past).
  • Requiring signature for W2/paper paystub delivery.
  • Positive: Accurate payroll tax calculation and reporting.
  • Positive: Enhanced efficiency and accuracy in running payroll.
  • Positive: Lower cost alternative for basic payroll services.
  • Negative: Slight difficulty in discerning pre-tax/post-tax deductions without the help of Paychex helpdesk.
Paychex Flex has been having longer than normal wait times, but I do think that it is a covid-related/staffing issue as it's only been happening in the past 2 months (November, December, January 2022). Once I do have a representative on the line, they are helpful, knowledgeable, and friendly. The support level is fairly basic at the representative level. For anything more complex, an HR specialist would need to be brought in.
Paychex flex was selected prior to my client contracting me. However, I have had the opportunity with other clients to evaluate, implement and administrate other payroll providers. Out of the products I've used, Paychex flex is most like Justworks. Paychex Flex is user-friendly and very basic but gives my client everything they need without additional bells and whistles (and cost!) It's a very good choice if you're looking for simple payroll administration.

Do you think Paychex Flex delivers good value for the price?

Yes

Are you happy with Paychex Flex's feature set?

Yes

Did Paychex Flex live up to sales and marketing promises?

I wasn't involved with the selection/purchase process

Did implementation of Paychex Flex go as expected?

I wasn't involved with the implementation phase

Would you buy Paychex Flex again?

Yes

Paychex Flex is very user-friendly. It is easy to run payroll and make manual adjustments where needed. It is simple to onboard new employees and off-board departing ones. It is also easy to make changes to current employee information in regards to leave, direct deposit info, deductions, tax status, etc.
Paychex Flex is a good software choice for small companies (11-50 people) with basic payroll needs. There is enough flexibility in the interface for the administrator to manually maneuver when adjustments need to be made, while also providing some "set it and forget it" features (ex. annual set per-pay-period deductions) and automatic payroll tax calculations.

Paychex Flex Feature Ratings

9.3
Employee demographic data
10
Employment history
10
Job profiles and administration
9
Workflow for transfers, promotions, pay raises, etc.
9
Organization and location management
9
Compliance data (COBRA, OSHA, etc.)
9
9.5
Pay calculation
9
Off-cycle/On-Demand payment
9
Direct deposit files
10
Salary revision and increment management
10
Reimbursement management
Not Rated
8.0
Approval workflow
8
Balance details
Not Rated
Annual carry-forward and encashment
Not Rated
8.0
View and generate pay and benefit information
8
Update personal information
Not Rated
View job history
Not Rated
View company policy documentation
Not Rated
Not Rated
Tracking of all physical assets
Not Rated
8.0
Report builder
Not Rated
Pre-built reports
8
Ability to combine HR data with external data
Not Rated
Integration with other HR capabilities ()
Not Rated
Performance Management ()
Not Rated
Succession Planning ()
Not Rated
Not Rated
Manager tracking tools
Not Rated
Performance and Goals ()
Not Rated
Recruiting / ATS ()
Not Rated

Relationship with Paychex, Inc.

The Paychex sales team was very willing to meet on our schedule, either virtually or in person. The non-profit I was consulting with was looking to reduce costs and one of the items on their list for consideration was changing payroll vendors. Although Paychex was a great product with excellent customer service, other providers were quoting reduced rates. After meeting with the Paychex sales team and explaining our situation, they were able to present a wonderful solution that kept all of the needed Paychex features while decreasing the total cost to the business. They were very willing to work with us and were able to keep us as a customer.
Paychex continues to have top notch self-service tools and technology. For the one to two times a year our business needs to call paychex, customer service is prompt, knowledgeable and pleasant to work with.
Negotiations resulted in reduced cost to the business while maintaining needed services. The non-profit's annual rate less than the previous year which was the determining factor in staying with Paychex Flex. One other payroll company did quote 1-year rate for slightly less than what we finally agreed to with Paychex, but given Paychex's customer service, our longstanding relationship and the potential for implementation hiccups with a new vendor, we were very happy to remain with Paychex.
Paychex is very easy to work with and is a very professional organization. I have no specific tips to effectively working with them, other than to take a problem-solving approach to negotiations vs. a hard line; Paychex is a customer solutions oriented organization and my sense is that by taking a cooperative vs. a combative approach to speaking with them you will reach a solution more efficiently.