Arrange a rack in the center of the oven and preheat to 350℉. Generously spray or butter a 9-inch deep-dish pie dish, then set aside.
Wash and dry the zucchini. Cut off the stem, then grate the zucchini using the coarse side of a box grater. Measure out 3 cups of grated zucchini and place it into a fine-mesh strainer and sprinkle with ½ teaspoon kosher salt.
Peel the onion and then grate it just as you did the zucchini; when it becomes cumbersome to grate, stop. Add the grated onion to the strainer with the zucchini, and gently stir to distribute the onion and salt. Let this mixture sit for 10-15 minutes while you prepare the rest of the ingredients.
In a large mixing bowl, whisk together the ¼ cup milk, 3 tablespoons all-purpose flour, and 1 teaspoon baking powder until smooth and thick.
Add 4 large eggs, ½ cup cottage cheese, ¼ teaspoon black pepper, ½ teaspoon garlic powder, and ½ teaspoon salt, and whisk to combine.
At this point, transfer the zucchini and onion to a clean kitchen towel or piece of cheesecloth and gently ring out excess moisture over the sink. Alternatively, use a spoon or measuring cup to very firmly press the zucchini and onion mixture into the fine-mesh strainer to remove excess liquid.
Add the drained zucchini and onion mixture to the egg mixture, along with the ¼ cup crumbled feta cheese and ½ cup Monterey Jack cheese, and fold together until evenly combined.
Transfer to the greased pie dish and bake for 40-45 minutes, or until the top is lightly browned and the eggs are set. The best way to determine if baked through is to take the internal temperature. Aim for about 165°F.
Let the pie sit for 15 minutes before slicing and enjoying.
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Notes
Cottage Cheese: Be sure to use full-fat cottage cheese for the best flavor and texture.Feta Cheese: Feel free to swap the feta for grated Parmesan or additional Monterey Jack.Monterey Jack: Feel free to use sharp cheddar in its place and grate from the block for the smoothest melt.Milk: Use cream, half-and-half, or any milk fat percentage you have on hand.Use a Food Processor: Make quick work of grating the zucchini and onion by using a food processor fitted with an S-blade.Storage: Store leftovers in an airtight container for up to 4 days and gently reheat as desired.