Ms. Athena Maria is absolutely right. The only way you can say (η αγαπημένη) is only you refer to the pizza and not the food category.
I baked your favorite (kind of) pizza.
Σου έψησα την αγαπημένη σου πίτσα.
Is exactly what Athena said, that the adjective follows the grammatical gender of the noun, I just wanted to give you an example!