Preheat your oven to 400F with a rack in the middle position.
Cut each bell pepper right down the middle. Clean out the insides of each bell pepper half, keeping the green stem intact. Place them in the baking dish, open side up.
In a large saucepan on medium heat, drizzle in the olive oil. Cook the chopped onion and garlic until the onions are translucid. Add the spinach to the pan and cook them until fully wilted.
Transfer the spinach mixture to a large bowl. Add to the bowl, the lemon zest and juice, the cottage cheese, the feta, dill, and the egg. Mix everything until well combined.
Divide the spinach mixture equally by filling all 6 bell pepper halves. Sprinkle the mozzarella cheese on top.
Cover the baking dish with foil. Place in the preheated oven and bake for 15 minutes. Remove the foil and continue baking uncovered for 10 minutes. You can place the dish under the broil if you want for of a crust on the cheese.
Remove from the oven and let rest for 5 minutes before serving hot.