The fact that you are employed by an "non-profit" employer does not mean that YOUR income is not taxable. If you owe tax due it is likely because you did not have enough tax withheld from your paychecks. You might want to change the W-4's that you provide to both employers so that they withhold enough tax.
https://turbotax.intuit.com/tax-tools/calculators/w4/ https://www.irs.gov/individuals/tax-withholding-estimator
https://www.irs.gov/pub/irs-pdf/fw4.pdf
https://turbotax.intuit.com/tax-tips/tax-payments/video-why-would-i-owe-federal-taxes/L3VXudPiN
You pay tax on your w-2 wages, even if you work for a non-profit. You have to enter all of your w-2s on your return. Since you already filed, you will need to file an amended return to add the second w-2. Wait until the original return is fully processed, and then use these instructions to amend your previously filed return.
Federal Taxes are not taken out as its a non profit organization, its always zero
@lily-hernandez Are they paying you as an independent contractor? Are they taking anything out for Social Security or Medicare? Did you receive a W-2 or a 1099NEC?
I did enter all my W2 - I just didn't mark the box that the 2nd job was a non profit.
There is not a box to say you worked for a non-profit. Working for a non-profit does not make your wages exempt from tax. It is unfortunate that no tax was withheld. That is likely the result of the amount you earned--and not because it was a non-profit. But when combined with your other income, you owe tax on the total amount of income you earned in 2023.