How can filing separately get me $2000 more filing jointly?

Where does it show that?  

Here's some things to consider about filing separately……

In the first place you each have to file a separate return, so that's two returns.  And if you are using the Online version that means using 2 accounts and paying the fees twice.  

Many people think they come out better when filing Married Filing Separate but they are probably doing it wrong.  If one person itemizes deductions on Schedule A then the other one must itemize too, even if it's less than the standard deduction, even if it is ZERO!  And if you are in a Community Property state it can be complicated to figure out.

And there are several credits you can't take when filing separately, like the

EITC Earned Income Tax Credit

Child Care Credit

Educational Deductions and Credits

And contributions to IRA and ROTH IRA are limited when you file MFS.

Also if you file Married Filing Separately up to 85`% of your Social Security becomes taxable right away even with zero other income.

See …….

https://ttlc.intuit.com/community/married/help/is-it-better-for-a-married-couple-to-file-jointly-or-separately/00/25590

To compare Joint to MFS.  If you are using the Online version, do NOT change anything on your return.  You would have to start with a new account and do a test return.  You don't have to pay unless you want to print it out.  So you might need 3 accounts, one for Joint and two MFS, one for each spouse.

If you are in a community property state, you would be required to have any common income split equally if you file separately.  They are Arizona, California, Idaho, Louisiana, Nevada, New Mexico, Texas, Washington, and Wisconsin. 

If you are not in a community property state, you have more flexibility but there are still some tax credits that will only be available if you file jointly. If you give up a tax credit, it could easily make a $2000 difference.  You may wish to mock up a return each way and see which would be most beneficial with your situation. 

This TurboTax Help article gives some examples of differences in filing married separately or jointly.

After clicking Federal Review, it verifies the information and the next tab shows the refund amount.  Below that, next to the “Tell us how you’re feeling” shows “You might want to file separately” and explains they did the math and I could get $2003.00 more than filing jointly

We would like to take a closer look at the situation you described.  Married Filing Separately can be more beneficial in certain cases.  If you would be willing, please provide us with a diagnostic copy of your Married Filing Joint tax file.  

The diagnostic file will not contain personally identifiable information, only numbers related to your tax forms.  To do so, follow the instructions below and post the token number along with which version of TurboTax you are using in a follow-up thread.

Use these steps if you are using TurboTax Online:

• Sign in to your account and be sure you are in your tax return.
• Select Tax Tools in the menu to the left.
• Select Tools.
• Select Share my file with agent.
• A pop-up message will appear, select OK to send the sanitized diagnostic copy to us.
• Post the token number here. 

If you are using a CD/downloaded version of TurboTax, use these steps:

• Select Online at the top of the screen.
• Select Send Tax File to Agent.
• Click OK.
• Post the token number here.

@bjeaton101282