Is my husband allowed to file as married filing separately even though I already paid quarterly estimated taxes for us as married filing jointly? If so, what do I do now?

[JulieR]

According to the IRS:

“If you and your spouse made separate estimated tax payments for 2018 and you file separate returns, you can take credit only for your own payments.

If you made joint estimated tax payments, you must decide how to divide the payments between your returns. One of you can claim all of the estimated tax paid and the other none, or you can divide it in any other way you agree on. If you cannot agree, you must divide the payments in proportion to each spouse's individual tax as shown on your separate returns for 2018.”

[retiree]

Should not be a problem as long as YOU did not file MFJ.  Understand that the quarterly taxs paid  as based on MFJ will not be sufficient if he files MFS and you also file as MFS.

[kelly-louise-goy]

Neither of us has filed yet. He just told me today that the finance office at his alma mater advised him to file MFS because of his school loans.

[retiree]

If his school loans are in arrears then you can still file MFJ, BUT you need to also file and 'Injured Spouse' form to protect your portion any refund there might be.