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  • Andrea Lyles, EA

QuickBooks Payroll Warning

Updated: 2 days ago

Here is the video version of this blog if you prefer to listen than read:


There are some issues that frequently come up when we are doing QuickBooks cleanups, and the payroll company being used can affect how difficult the clean up will be. I don't take it lightly to give a warning such as this one, but we have just seen too many issues to keep quiet about it.


I can see where you might think that if you have QuickBooks Online, it would only make sense to use QuickBooks for your payroll as well. While I do recommend QuickBooks Online as an accounting solution, I cannot recommend their payroll solutions. Whenever we’ve had a clean up client come to us with a previous or existing QuickBooks Payroll subscription, it is extremely difficult to clean up the related issues. The reason is that once the payroll has been run, it’s impossible to go in and retroactively make adjustments to the mapping of associated bank accounts. So if this has gone on for months or years, and it was mapped to the wrong account, there’s a lot that needs to be done to have the transactions match to the right account. If this were to happen with other payroll integrations, we are at least able to access the journal entries and make any adjustments that need to be made. That in itself saves a lot of time in the clean up.


While the above mentioned is the most frequent issue we see, it's definitely not the only one. QuickBooks Payroll is known within the bookkeeping community to suffer with bigger issues, such as deposits not being made, erroneous tax reports, etc. Their customer service would definitely have to get involved in those situations, and let's just say speediness is not one of their better attributes. It can take many months to see your problem(s) resolved.


We provide the following recommendations: Have a professional set up your payroll. Choose a reliable payroll company. While every company has slightly different needs, the following are highly recommended companies: OnPay, Patriot Software, or Payroll4Construction (great if you need job costing or construction-specific features). We also have never had an issue with actual payroll runs in Gusto, but I do have to say that their customer service took a downturn during the pandemic, and their recent price hike doesn't reflect the level of service currently provided. Hopefully they will make a comeback.


If you have any questions, feel free to book a call with us. We provide free 30 minute consultations and may be able to point you in the right direction regarding your payroll needs.


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