Hi @Clae
Time separated does not count as part of the three years required for an independent right of residence. The independent right of residence is covered in paragraph 31 of the immigration law (Aufenthaltsgesetz). In section one of this you can see that the law refers to the marriage partnership (in German ‘eheliche Lebensgemeinschaft)) having existed for at least three years. It is not enough to be married for three years, you also must also have living as partners.
Here is the legal text in English via online translation:
https://***-gesetze--im--internet-de.translate.goog/aufenthg_2004/__31.html?_x_tr_sl=de&_x_tr_tl=en&_x_tr_hl=en&_x_tr_pto=wapp
The exception to this three-year requirement is detailed in section two of that law. In cases where it is unreasonable to expect a person to remain in a marital partnership, they can be given an independent right of residence after less than three years. This applies in particular in cases involving domestic violence.
Best,
Éanna