Spread grated zucchini and chopped mushrooms on a large cookie sheet. Sprinkle with salt and let sit for about 15 minutes to disgorge excess moisture from the vegetables. Gently squeeze remaining moisture from mushrooms and zucchini, discarding liquid.
Preheat oven to 350. Line a large cookie sheet with parchment paper.
In a large mixing bowl, beat two eggs. Mix in almond flour, minced garlic, thyme, black pepper and red pepper flakes, if using. Add mushrooms and zucchini and stir to combine.
Using a half cup measuring cup, scoop batter onto the lined cookie sheet and gently form patties with your hands. Bake for 10 to 15 on one side, then carefully flip the patties and bake for 10 to 15 minutes on the other side. Burgers will take on a golden brown color as the egg sets up. Let cool before serving.
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