Start by preheating your oven to 400°F (200°C).
In a microwave-safe bowl, combine the mozzarella and cream cheese. Microwave for 1 minute, then stir well. Continue microwaving in 30-second intervals, stirring after each, until the cheese is completely melted and smooth like a fondue. Next, add the almond flour, coconut flour, baking powder, and egg. You can mix this by hand on wax paper or use a food processor with a dough blade until everything is fully combined into a soft, uniform dough.
Divide your dough into two equal portions. With slightly wet hands, press each portion into a rectangular shape on a baking sheet lined with parchment paper. Bake these flatbread bases for 10 minutes.
While the dough bakes, heat the olive oil in a large frying pan over medium-high heat. Sauté the thinly sliced onions until they become beautifully softened and caramelized to a golden brown.
After 10 minutes, take the flatbread bases out of the oven. Layer 3 slices of pepper jack cheese on each, followed by 3 slices of mild cheddar. Then, evenly distribute the chopped cooked chicken and the sautéed onions over the cheese. Return the flatbreads to the oven for another 8-10 minutes, or until the cheese is bubbly and melted, and the toppings are heated through.
While the flatbreads finish baking, prepare your zesty lime crema. Whisk together the sour cream, fresh lime juice, and a pinch of salt. For an easy drizzle, transfer this mixture to a zip-top bag and snip a small corner off.
Once the flatbreads are ready, remove them from the oven. Drizzle generously with the homemade lime crema, sprinkle fresh chopped cilantro over the top, slice into portions, and serve immediately. For an extra kick, a dash of crushed red pepper flakes is a great addition!