“Is anyone run payroll for two completely separate companies in QuickBooks Desktop Enterprise and can share how you managed it?”
Hi, I’m Berry Kitty. I run two small businesses — one’s a design consultancy and the other is a local retail store. Both are legally and financially separate, and I maintain individual company files for each in QuickBooks Desktop Enterprise.
I recently purchased Enhanced Payroll thinking it would simplify things. Payroll setup worked fine for my first company. But when I opened the second company file and tried to enable payroll there, I ran into multiple problems.
First, QuickBooks prompted me to “Add this company to your existing payroll subscription.”
But when I clicked yes, it threw an error saying something like “This EIN is already in use” — which made no sense because this is a completely different business with its own EIN.
I tried calling support, but I got mixed messages — one rep told me I’d need a second payroll subscription, while another said it might work if I toggle between files a certain way. Super confusing.
I also worry that if I somehow link both companies to one payroll setup, it might mess up tax filings or employee records — especially since both companies have different pay schedules and benefit structures.
What I’m trying to figure out is:
Can one Enhanced Payroll subscription actually support two company files with different EINs?
If not, is there a workaround that doesn’t involve paying double?
Has anyone here faced this before and managed to set up payroll in both companies without any data conflict?
I’d love to hear from someone who’s been through this. This is slowing down my year-end prep and making me nervous about compliance.
Yes, Berry Kitty — you can run payroll for two separate companies, but not under a single Enhanced Payroll subscription in QuickBooks Desktop Enterprise. Since each of your businesses has a unique EIN and separate company file, QuickBooks treats them as completely distinct entities, which means each one requires its own payroll subscription.
Running payroll in QuickBooks Desktop Enterprise is usually straightforward when you’re working with one company. But things can get tricky and confusing when you’re managing payroll for two separate businesses — each with its own Employer Identification Number (EIN).
Many business owners assume they can use a single Enhanced Payroll subscription to handle both companies. After all, both are managed by the same person, and the software is installed on the same system. But when they try to activate payroll in the second company file, they see an error like “This EIN is already in use.”
Why You’re Seeing the “This EIN is Already in Use” Error
When you activate Enhanced Payroll, QuickBooks links your subscription to the first EIN you use during setup. This means that EIN becomes permanently associated with your payroll license and is used for all payroll-related functions including tax filings, employee records, and benefit reporting.
So, when you open a second company file with a different EIN and try to enable payroll using the same subscription, QuickBooks blocks the process. That’s when you see the error:
“This EIN is already in use.”
It’s not a system bug, it’s a compliance safeguard. QuickBooks is designed to ensure each payroll subscription is tied to only one legal entity. This prevents critical errors like misfiled tax forms or employee data mixing between businesses.
Can Basic or Standard Payroll Avoid This?
You might think that switching to Basic or Standard Payroll could bypass this restriction, but unfortunately, that’s not the case. Both Basic and Standard Payroll are also licensed per EIN. They follow the same rule as Enhanced Payroll:
One EIN = One Payroll Subscription
Even though these versions offer fewer features (like no automated tax payments or filings), the core licensing structure doesn’t change. You’ll run into the same error if you try to use one subscription across two EINs — regardless of the payroll tier.
Why QuickBooks Enforces This Rule (And Why It Actually Helps You)
QuickBooks doesn’t impose the “one subscription per EIN” rule just to sell more services — it’s actually doing it to protect both you and your business from serious legal and tax complications. Let’s break down why this matters and how it works behind the scenes.
QuickBooks payroll services are designed to stay in strict alignment with IRS and state payroll regulations. One of the key rules is that each business entity — defined by its unique EIN (Employer Identification Number) — must keep separate payroll records.
If multiple EINs were allowed under one subscription, QuickBooks could accidentally:
- Submit tax forms for the wrong business
- Mix employee earnings across companies
- File with the wrong state and federal agencies
This would trigger red flags with the IRS and state departments — possibly leading to audits, fines, or even legal issues.
What Could Go Wrong Without This Rule?
If QuickBooks allowed multiple EINs under one payroll setup, here are just a few things that could go off track:
- Wrong Tax Filings: Form 941 or 940 could be filed under the incorrect EIN, causing misreporting of payroll taxes.
- Incorrect W-2s or 1099s: Employees might get forms with the wrong company name or tax ID — creating confusion for them and liability for you.
- Misrouted Payments: Payroll taxes might be withdrawn from the wrong business bank account.
- Audit Failures: During IRS or state audits, inconsistent records could trigger penalties or non-compliance notices.
FAQs
Can I Change an Employee’s Pay Schedule in QuickBooks Desktop After Initial Setup?
Yes, you can change an employee’s pay schedule at any time in QuickBooks Desktop. Simply:
- Go to the employee’s profile
- Select “Payroll Info”
- Update the pay frequency (weekly, biweekly, monthly, etc.)
However, make sure to process any pending payroll under the old schedule before switching, to avoid calculation errors or missed deductions.
Can I Run Payroll Manually in QuickBooks Desktop Without Purchasing a Payroll Subscription?
Yes, you can manually run payroll in QuickBooks Desktop by turning on manual payroll calculations in the preferences. This allows you to enter employee hours, calculate payroll taxes externally, and enter the amounts into QuickBooks. However, you won’t have access to automated tax form generation, e-filing, or direct deposit, and you’ll be fully responsible for calculating and submitting payroll taxes correctly.
What Happens to My Payroll Data If I Cancel My QuickBooks Payroll Subscription?
If you cancel your payroll subscription, you’ll retain read-only access to historical payroll data in your company file. However, you will no longer be able to:
- Process new paychecks
- File payroll tax forms
- Access updated tax tables
- Use direct deposit
To maintain compliance or retrieve records later, it’s essential to export payroll reports and save backups before canceling.
Disclaimer: The information outlined above for “Can I Run Payroll for Two Separate Companies with Different EINs Using QuickBooks Desktop Enhanced Payroll?” is applicable to all supported versions, including QuickBooks Desktop Pro, Premier, Accountant, and Enterprise. It is designed to work with operating systems such as Windows 7, 10, and 11, as well as macOS.