Pricing. Paychex Flex lists Flex Essentials at $39 a month plus $5 per employee; its other packages are quoted, and tax administration, W-2s and 1099s may cost extra on Essentials. ADP RUN quotes every package and charges more as payroll frequency rises.
Capabilities. Both cover payroll, tax filing, contractor payments, HR tools and add-on benefits. ADP RUN adds bill pay and invoicing and applicant tracking by CareerPlug; Paychex Flex adds time and attendance and workers' compensation modules.
Integrations. Paychex Flex offers a REST API with webhooks and lists QuickBooks, Sage Intacct, Xero, NetSuite, When I Work and 7shifts among its integrations. ADP RUN connects to QuickBooks, Xero, Wave, Creative Solutions, Clover and ZipRecruiter.
Fit and support. ADP RUN offers 24/7 payroll support by phone or chat; Paychex lists 24/7 payroll support, with a payroll specialist on its Complete package.
Security. Neither names a security certification on the product pages we reviewed.