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Year End FAQs: 1099s and W-2s

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In our journey to prepare you for all things Year End, I want to take some time to focus on 1099 and W-2 forms. While they are used for different workers, both are equally important to understand. Let’s start with a quick overview of the difference between the two.
The IRS 1099 Form is a collection of tax forms (QuickBooks primarily deals with NEC and MISC) documenting different types of payments made by an individual or a business to those workers that are not employees. 1099 workers are considered to be self-employed or independent contractors, and therefore do not have taxes withheld as part of their payment.

The individual or business paying the contractor is the one that fills out the form with the appropriate details and sends copies to the IRS, reporting payments made during the tax year, and to the independent contractor who performed the work, who receives a 1099 form to report their income on their tax returns. In contrast, W-2 forms are for employees that work for you directly, and they receive regular pay and employee benefits. You’ll use a W-2 tax form to report their annual compensation and payroll taxes withheld to the IRS. 

Still not sure? Take a look at our helpful article dedicated to this subject: W2 vs 1099: What’s the Difference?

Now that we have covered the basics, let’s move forward and look specifically at W2s. 



To give your employees access to their current year (and previous two years) of W-2s, you’ll want to invite them to use QuickBooks Workforce. If they don’t see the forms there, don’t worry. Depending on the payroll service you use, W-2s aren't immediately available on January 1. W-2s are automatically sent to QuickBooks Workforce once Intuit files them and will typically be available after January 15. Take a look at our Year End Dates calendar for important deadlines based on your product.

Your employees will automatically get W-2 forms mailed to them by USPS starting January 20 through January 31.

Note: Does your accountant need a copy of your W-3? You can print one out for them from your account. 

If you use QuickBooks Online and are wondering who creates your W-2s and sends them to your employees, it depends on your payroll service.  There are two methods:

  • We file and send your W-2s to your employees, the IRS and SSA for you
  • Or, you file your W-2s with the IRS and SSA, and then print and send them to your employees

Check out this article to find your payroll service and see what steps you need to take: Understand the timing for W-2 filing, delivery, and access for you and your employees.

Don’t worry! I didn’t forget about our Desktop customers. In this case, e-filing is dependent on the state your company is in. Here’s the article for you: File your state W-2s with Quickbooks Desktop Payroll Enhanced.


Now let’s switch gears and talk about 1099s. Let’s start with 1099-NEC and 1099 -MISC.

If you are paying contractors or vendors, you may need to provide them with a 1099. The IRS has separated non-employee compensation into two forms called the Form 1099-NEC and Form 1099-MISC.

  • Form 1099-NEC
    • Box 1 will not be used for reporting under section 6050R, regarding cash payments for the purchase of fish for resale purposes.
    • Box 2. Payers may use either box 2 on Form 1099-NEC or box 7 on Form 1099-MISC to report any sales totaling $5,000 or more of consumer products for resale, on buy-sell, deposit-commission, or any other basis. For further information, see the instructions later for box 2 (Form 1099-NEC) or box 7 (Form 1099-MISC).
    • Form 1099-NEC resized. We have reduced the height of the form so it can accommodate 3 forms on a page.
  • Form 1099-MISC:
    • Title has been changed from Miscellaneous Income to Miscellaneous Information.
    • New Box 11. Fish Purchased for Resale

Any additional questions, check out the IRS resource here: Instructions for forms 1099-MISC and 1099-NEC.

Now we can focus on how to get your 1099s ready to e-file or print. At this point, you’ve already created your vendor/1099 profile in your account so the steps below walk you through organizing your contractors and payments so your filings are correct.

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  1. Go to the Payroll menu, then select Contractors. Or select Expenses and then Vendors > Pay Bills Dropdown.
  2. Select Prepare 1099s and then Let’s get started.
  3. Make sure your company name, address, and tax ID is correct and matches what's found on tax notices or letters from the IRS.
  4. Select the boxes that represent the type of payments made to all of your contractors this year, then select Next. Important: There are changes to the 1099 forms and boxes, so choose your boxes carefully
  5. Verify that all of your contractors show up and their personal info and email addresses are correct.
  6. Review the payment totals for each box you selected in step 4. The payments will be automatically separated between the 1099-NEC and 1099-MISC forms. Select Next.
    • Note: You won't see payments that you made electronically to contractors (such as by credit card, etc.). This is because these are reported for you by the credit card company, bank, etc. If you don’t see all of the payments you expect, you can verify the year and threshold just above the Name column.
  7. Select E-File for me to e-file your 1099s. Or select I’ll file myself to print and mail the forms yourself.


The steps for QuickBooks Desktop, including E-file and printing, can be found here: Create and file 1099s with QuickBooks Desktop.

Once you have prepared the 1099s, you can send them to your contractors, but to file online with the IRS you need to complete the e-file process.

At some point in this process, you may run into a roadblock. Why don’t I see a certain vendor? Why are the amounts not accurate? Not only do we have a whole article dedicated to these kinds of questions,  but I'll also go over some common reasons here. 

  • Your contractor isn't active or hasn't been set up for 1099 tracking

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  • Your payments to that contractor(s) haven't met the annual $600 cash threshold to get a 1099
  • You’re paying contractors from the wrong expense account. Note: When creating 1099s, QuickBooks uses the expense accounts you mapped to report 1099 transactions. If your amounts are off, you may want to review the contractor payment transactions and accounts associated with them. 

Keep in mind we have a lot of report options to help you see your contractor transactions. Just go to Reports on your Left menu and search or scroll through:

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Other resources for tracking 1099 accounts (both Online and Desktop):


Lastly, I’m going to link a quick infographic that explains changes to the Form 1099K.  Keep in mind, gross amount refers to the total dollar amount of all reportable payment transactions, without regard to any adjustments for credits, cash equivalents, discount amounts, fees, refunded amounts, or any other amounts. For more information see IRS instructions for 1099-K. Consult your Tax Professional or IRS for the best way to report adjustments.

Full information on this form and state requirements/exceptions can be found in this article: Intuit 1099-K form.

And there you have it! Stay tuned for the next Year End article to help you stay on track this tax season. 

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