Preheat oven to 375°F and line a baking sheet with parchment paper.
In a large bowl, combine ground beef, almond flour, eggs, Parmesan cheese, Italian seasoning, garlic powder, salt, pepper, and 1/4 cup marinara sauce, mixing gently until just combined.
Place half of the meat mixture on the prepared baking sheet and shape into a flat rectangle about 1 inch thick.
Layer 1/2 cup mozzarella cheese and the diced pepperoni down the center of the meat rectangle.
Cover with the remaining meat mixture, pressing and sealing the edges to completely enclose the cheese and pepperoni filling.
Shape into a traditional loaf form and spread the remaining 3/4 cup marinara sauce over the top.
Bake for 50-55 minutes until the internal temperature reaches 160°F.
Remove from oven, top with remaining 1/2 cup mozzarella cheese, and return to oven for 5 more minutes until cheese is melted and bubbly.
Let rest for 10 minutes before slicing and serving.