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Best QuickBooks compatible Payroll Service for Accountants

Intuit Online Payroll for Accountants VS. QuickBooks Enhanced Payroll for Accountants

As an accountant offering Payroll Services having a good system or software is the backbone of my payroll operation. But I have to admit, the scope of work of this “payroll service” tends to be all over the map as the amount of attention required from be greatly varies client by client.

I have asked many of my colleagues, and they seem to agree with me that Payroll is one of the most unpredictable services they offer.  And other of my colleagues will admit to preparing any and every tax form out there, with the exception of payroll.

The truth is, that payroll services can add a significant and steady (monthly/quarterly) income stream to the firm while additionally strengthening the relationship with the client making the accountant even more indispensable to their clients.  The downside is the unpredictability that may arise from issues and changes within a company’s internal payroll, potentially creating non-billable service time.

Myself, being QuickBooks driven, I naturally chose QuickBooks Enhanced Payroll for Accountants (EP4A) as my system of choice to provide this service.  The main features that attracted me to this choice are:

  1. Price, its $429 per year (or $200 as an upgrade to the annual ProAdvisor Membership)
  2. Ideal for the amount of clients I  was managing, under 50 EIN’s
  3. Seamless  integration within QuickBooks
  4. After-The-Fact gave me full control of input and adjustments before filling forms or paying taxes



As my practice (and clients) grew, certain situations created some constrains on working with an After-The-Fact system, such as:

  • Clients that want to input their own timesheets within QuickBooks and generate Payroll Internally
  • Time constrains (during busy time or after hours) to respond to clients on questions about special situations that requires paycheck calculation beyond the pre-established amounts or pay periods
  • Clients that wanted to control the exact date a direct deposit check is debited or tax payment is debited

Luckily, I did not have to look too far to find an alternative that will allow me to service these clients.   The whole outlook of payroll services as I knew it changed when I implemented Intuit Online Payroll for Accountants (IOP4A).  Some of the differences are very obvious such as IOP4A is completely web-based, so I did not have to be in my computer with QuickBooks open with the client’s company in order to process payroll, which gave some new dynamic to be able to service my payroll clients from home or on the road much faster.   Additionally, the clients get access too, which allows the client and me to collaborate in payroll efforts, for instance:

  1. My client will login into IOP4A and enter the hours and bonus for a particular employee and create the paycheck AND print it, they can even create direct deposit paychecks
  2. I can login the system at any time and make any adjustments and/or create the tax payments

With some clients, I have completely delegated all the payroll tasks such as creating paychecks, adding new employees, making tax payments, etc… And I simply just e-file the tax forms.  This has allowed me to maintain my “needy” clients without increasing my prices or dedicating much non-billable service time.  There are some other distinct advantages to this payroll system in comparison with EP4A:

  • Direct Deposit for up to 150 employees is no additional cost, vs. $1.25 on EP4A.  This is a huge price advantage for some of my larger clients that thought our payroll service costs too high mainly due to Direct Deposit fees which were not generating any additional revenue to my firm
  • The system is web-based and open 24/7 which allows my clients to at least create and calculate paychecks at any time, giving me the flexibility to login on my time to make are revisions or adjustments if necessary
  • As long as the service is active, the clients may have access to viewing the tax forms, which reduces all those requests for copies of old 941’s or W-2’s
  • All the clients are in one login, which makes it very quick to switch from client to client to service their payroll
  • It is “white labeled” which gives the impression that the payroll system exclusive to my firm, nowhere it says it’s Intuit.
  • Clients that want to be able to delegate payroll tasks to a staff member without giving them ANY access to QuickBooks


But it also important to identify that IOP4A will not be for every client, for example these are the reasons I may choose to keep my client on EP4A:

  • Need detailed job costing and class information to be generated from each check
  • Need to generate specialized Payroll reports only available within QuickBooks
  • Seamless QuickBooks integration is required because timesheet data is being imported in QuickBooks via IIF on app integrated to QuickBooks Desktop edition
  • Fast calculation of gross pay by simply inputting net pay

And there are some situations where neither solution was available, such as a client wanting to process their own payroll in its entirety… Then I just recommend QuickBooks Enhanced Payroll, and just get involved with the client in support and training their staff to process it correctly.

Today, I find myself working with the 3 Payroll options Intuit offers:

QuickBooks Enhanced Payroll: for clients wanted to control all aspects for their payroll, seamlessly integrated within QuickBooks not needing my accounting services periodically.

QuickBooks Enhanced Payroll for Accountants: for clients that need After-The-Fact payroll services and detail payroll data must stay integrated within QuickBooks

Intuit Online Payroll for Accountants: for clients that would prefer to have an online portal to generate paychecks and payroll taxes, while keeping control (as accountant) of what gets filed to IRS and States.


My default service of choice is actually IOP4A, primarily because I prefer to give my clients more “control” which means less “work” for me in the long run.


Hector Garcia

Hector Garcia

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