Fill a large a large Dutch oven or deep fryer with 3 inches of oil. Heat the oil to 350 degrees F.
Cut the onions crosswise into 1/2-inch-thick slices and separate into rings. Using 2 rings that will fit inside one another, sandwich a slice of cheese and a slice of pepperoni between the rings and press together. Repeat.
Place 1/2 cup of the flour in a shallow dish. In a large bowl, whisk together the remaining 1 1/2 cups flour and the Italian seasoning and garlic powder. Slowly whisk in enough beer to produce the consistency of a thick pancake batter. Season with salt and pepper. Let rest for 5 minutes.
Gently dredge the stuffed onion rings in the flour and then dip in the batter. Fry in batches until golden brown, 2 to 3 minutes. Sprinkle with salt and Parmesan.
Serve immediately, with marinara sauce on the side.