Preheat oven to 425F. Prepare a double boiler using a pot partially filled with water with a mixing bowl that fits well on top. Bring the water in the pot to a simmer over high heat and then turn the heat down to low.

In the top part of the double boiler, add the mozzarella, cream cheese, almond flour, thyme, and salt. Place the bowl over the simmering pot of water and stir constantly. A silicone mitt works well for holding the bowl and avoiding burns from the hot steam.

Once the cheese has melted enough that the ingredients hold together and it starts to resemble dough, dump the mixture out onto a piece of parchment paper. Knead for a few minutes to combine the dough thoroughly.

Roll the dough into a ball and place in the center of the parchment paper. Pat it into a disk shape and cover with the other piece of parchment. Gently roll the dough into a circle. If the bottom parchment paper begins to crease, turn the dough over and straighten the parchment paper before continuing.

Place the dough and the bottom piece of parchment paper onto a pizza pan. Using a fork, poke holes in the top of the dough. Place the pan in the oven and bake for about 6–8 minutes, watching carefully. Remove from the oven once golden brown. Decrease the oven temperature to 350F.

Sprinkle one-quarter of the cheese over the flatbread. Layer on the sliced onion, apple, and ham. Cover with the remaining cheese. Sprinkle the thyme, salt, and pepper over the top.

Bake for 5–7 minutes, until the cheese is melted and the crust is golden brown. Let cool for a few minutes before slicing.