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Paychex Flex vs Pilot

Paychex Flex logo

Paychex Flex

Software

Payroll and HR solutions that grow with you

From
$39/month
Rated
-
Full reviewWebsite
Pilot logo

Pilot

Software

Bookkeeping, CFO, and tax for startups

From
$29/month
Rated
-
Full reviewWebsite

The short version

  • Each has a real cost: Paychex Flex paychex publishes no rate card for Paychex Flex: the payroll page names the Select, Pro and Enterprise packages but gives no per employee fee, no base monthly fee and no setup fee; Pilot the Essentials bookkeeping plan at $99 per month covers up to $100,000 in monthly expenses, and is cash-basis only using bank and credit card data
  • They diverge on capability: Paychex Flex covers Payroll Processing, Pilot covers Bookkeeping.

Where they differ

Only the attributes on which Paychex Flex and Pilot actually diverge.

Attributes where Paychex Flex and Pilot differ
AttributePaychex FlexPilot
Starting price$39/month$29/month
Pricing modelquotesubscription
PlatformsWeb, Ios, AndroidWeb
Founded19712017

Identical on both: free tier (No), user rating (Not yet rated), category (Unknown).

What each one covers

Drawn from each product's published feature list. An absence here means we hold no record of it - not that the product lacks it.

Only in Paychex Flex

  • Payroll Processing
  • Tax Administration
  • HR Services
  • Benefits Administration
  • Time and Attendance
  • Retirement Services
  • Xero
  • Sage

Only in Pilot

  • Bookkeeping
  • CFO services
  • Tax preparation
  • R&D tax credits
  • Financial reporting
  • Stripe
  • Brex
  • Gusto

Both cover

  • QuickBooks
  • Web support

What people use each for

The jobs each tool is most often brought in to do.

Paychex Flex

  • Running payroll and filing payroll taxes for small and mid sized US businessesnot Pilot
  • Combining payroll with benefits administration and HR services from one vendornot Pilot
  • Handling multi state payroll compliance and year end tax formsnot Pilot

Pilot

  • Outsourced monthly bookkeeping for startups and small businessesnot Paychex Flex
  • Federal, state and Delaware franchise tax filing for US companiesnot Paychex Flex
  • Fractional CFO support for financial planning and fundraisingnot Paychex Flex

Where each one falls short

Documented limitations, not opinions. Every one is a constraint you would hit in normal use.

Paychex Flex

  • Paychex publishes no rate card for Paychex Flex: the payroll page names the Select, Pro and Enterprise packages but gives no per employee fee, no base monthly fee and no setup fee
  • Pricing is obtained only by requesting a quote or calling sales
  • Product capability is split across three packages, so features are tied to a tier whose price is not disclosed

Pilot

  • The Essentials bookkeeping plan at $99 per month covers up to $100,000 in monthly expenses, and is cash-basis only using bank and credit card data
  • A dedicated US-based bookkeeper, accrual-basis books and phone support require the Core plan, which is contact sales and billed annually
  • Core caps bill management at 10 vendor bills per month
  • Keeping an existing QuickBooks account with historical data requires the Custom plan
  • Accounts receivable, accounts payable, payroll administration and CFO advisory are Custom plan only
  • Monthly reports arrive on the 10th business day on Core and the 6th business day only on Custom
  • Tax filing is sold separately, starting at $1,000 per year for single member LLCs and $2,000 per year for partnerships and S-Corps, billed annually
  • The tax service must be purchased together with Pilot Bookkeeping
  • Partnership and S-Corp tax filing includes up to 25 1099-NEC filings

Pricing, plan by plan

Paychex Flex

$39/month
  • Essentials$39/month
    • Payroll Processing
    • Tax Services
    • Direct Deposit
  • Select$undefined/month
    • All Essentials features
    • HR Administration
    • Onboarding

Pilot

$29/month
  • Core$599/month
    • Bookkeeping
    • Accrual basis
    • Monthly close
  • Plus$849/month
    • CFO support
    • Custom reporting
    • Board deck

Which should you pick?

Choose Paychex Flex if

  • You need payroll processing.
  • You work on Web, Ios, Android.
  • You also want tax administration.
Paychex Flex review

Choose Pilot if

  • You need bookkeeping.
  • You also want cfo services.
Pilot review

Questions people ask

Is Paychex Flex or Pilot better?
Neither clearly leads. Paychex Flex starts at $39/month and Pilot at $29/month, and user ratings are close enough to be indistinguishable. Choose on capability and platform support.
Which is cheaper, Paychex Flex or Pilot?
Paychex Flex starts at $39/month and Pilot at $29/month.
Does Paychex Flex or Pilot run on more platforms?
Paychex Flex runs on Web, Ios, Android. Pilot runs on Web.
What is Paychex Flex best used for?
Paychex Flex is most often used for running payroll and filing payroll taxes for small and mid sized us businesses, combining payroll with benefits administration and hr services from one vendor, handling multi state payroll compliance and year end tax forms. Of those, running payroll and filing payroll taxes for small and mid sized us businesses and combining payroll with benefits administration and hr services from one vendor are not what Pilot is typically brought in for.
What can Paychex Flex do that Pilot cannot?
Paychex Flex covers Payroll Processing, Tax Administration, HR Services, Benefits Administration. Pilot covers Bookkeeping, CFO services, Tax preparation, R&D tax credits. Both handle QuickBooks, Web support.
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