Place the 3 cups cauliflower rice in a large microwave-safe bowl and microwave 2–3 minutes until tender.
Drain the cauliflower thoroughly and press or squeeze out all excess moisture, then transfer to a large mixing bowl.
Add 6 tablespoons almond flour, 2 egg yolks, and 1 cup grated Parmesan to the cauliflower and mix until evenly combined.
In a separate microwave-safe bowl, microwave the 2 cups shredded mozzarella until melted, then pour the melted mozzarella into the cauliflower mixture and mix until fully incorporated into a cohesive dough.
Lightly wet your hands and divide the dough into 4 equal portions; roll each into a ball, place on a plate, cover, and refrigerate 10 minutes to firm.
Lightly dust a clean work surface with almond flour. Roll each chilled ball into a thin log and cut into bite-sized pieces.
Use a fork to gently press each piece to create ridges, then place the formed gnocchi on a plate and refrigerate, covered, for 20 minutes.
Bring a large pot of salted water to a boil. Add the gnocchi and cook for 1 minute once the water returns to a boil.
Drain the gnocchi well and serve immediately with your preferred sauce.