1099 Processing for multiple EINs


The system can accommodate tracking and printing 1099 forms for more than one company and EIN#. Instructions as follows:

  • Go to Setup > 1099 Codes. This table assigns the box# and form type where the specific code will print and be reported.
    • You will want to add the same code for each company. For example, if you have two companies, you would add a code N=Non Employee Compensation (Form 1099-NEC) for Company 1, as well as a code N2=Non Employee Compensation (Form 1099-NEC) for Company 2. The codes can be names of your choice. See Help for 1099 Codes for details.


  • Go to Setup > Exports > 1099 Formats. You must have a federal format for each company. Add a federal format for Company 1 and a second federal format for Company 2. The names can be anything you choose. Both 1099-MISC and 1099-NEC reporting will use the same federal format.
    • Edit the format and select Line Type “Paper Form”. Enter the company name/address information, as well as phone and Federal ID. Save the format.  This information will be used for printing on the form, as well as on the electronic file for this company.
    • Select Line type “File Header” and enter the Transmitter Control Code, Contact Name, Phone#, and Email Address. Nothing else needs to be changed on this screen.
  • On the 1099 Browse screen, when tagging payments for 1099 reporting, tag the amounts with the appropriate code (ie. N vs. N2) to represent Company 1 vs Company 2.
  • On the 1099 Browse screen, you may filter what is displayed by clicking on Tagged Codes and selecting the codes for Company 1 or Company 2. Click Display to refresh the screen. This will help you to analyze the reportable payments by company and by tagged code. Click Reports drop down arrow to export anything displayed on the screen to Excel.
  • When printing the forms, select the Year and the Form type (MISC, NEC, etc.); also the appropriate format for printing (Company 1, Company 2, etc.)

Note: Forms are printed based on what is tagged for printing on the appropriate form, regardless of what is filtered at any time on the 1099 Browse screen.