Yes, you can file separately at any point even when you live together.
However, if one person does not have any income, then tax wise, you will make out better by filing a joint return. When you file separate returns, there are several tax credits and deductions you cannot take such as education credits, and the earned income credit. Also, the standard deduction is half what it would be if you file a joint return. This means if only one person is working and makes $50,000 a year, if they file as married filing jointly, they will only pay taxes on $19,8000 whereas, if they file separately, they will pay taxes on $35,400 of their income.
Overall, if you are in the same household, when it comes to strictly a tax perspective, in general, it is better to file a joint return.
How Should You and Your Spouse File Taxes? Married Filing Jointly vs Separately
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