Yes, TurboTax can handle returns where spouses are residents of different states and it also allows you to designate which income belongs to which spouse in most cases to aid in how it flows to the state returns. However, there will still likely be some manual adjustments required.
The mechanics of how the two separate states are handled depends on which states are involved.
You can confidently start your returns in TurboTax knowing it can handle this, and please post a new question here if you have any concerns about how to prepare your state returns.
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