I wanted to try making a lot of food at once and freezing it, so meals will be faster throughout the week. My question is can you freeze tomatoes and mushroom caps?

I wanted to stuff them with quinoa, ground meat, and an assortment of veggies.

You can freeze tomatoes, mushrooms get weird frozen. Maybe freeze the filling in muffing tins or ice cube trays and add to mushrooms later?

If they are raw tomatoes they are going to weep liquid out of the freezer BUT maybe if you pop them in the hot oven from the freezer like lots of major brand frozen foods tell you to do they will work. I would just make a few as a test run