Yes. If you are filing a joint federal return in a TurboTax online product, you will not be able to create a separate state return with that account. You have three options.
1. Create/e-file a separate federal return and a separate NY return in one online product and open another account with a separate federal and state return for your spouse.
2. Create/e-file a joint federal return (and if needed a joint state return that is not NY) in one online account and open another online account in which you create a "Mock" separate federal return that can be used to create the separate NY return. You will need to print/mail the NY separate return as the "Mock" federal separate return will not be filed.
3. Use a desktop (CD/download) product. Create/e-file a joint federal return and, if needed, a joint resident state return (not NY) and then create a "Mock" federal separate return that will be used to create a separate NY return all in the same product. The NY state return will need to be printed/mailed.
Typically, option 3 is works the best. Here is a link with more details.
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