Preheat oven to 400 degrees F. Line a baking sheet with parchment paper and set aside.
Cut the top off the small pumpkin, peel, slice in half, and remove the seeds. Dice the pumpkin into 1" cubes. Transfer to the lined baking sheet and drizzle with 1 tbsp of the olive oil. Toss with a spatula or your hands and add salt and pepper to taste. Bake for 20-25 minutes or until fork-tender.
In the meantime, core and dice the apples. In a small bowl, whisk together the eggs, milk, cinnamon, salt, and pepper.
When the pumpkin is finished cooking, heat the last 2 tbsp of olive oil in a 12-inch skillet (cast iron or another oven-safe kind) over medium-high heat. Add the diced apples and cook for 3-4 minutes. Add the pumpkin and use a spoon to spread the pumpkin and apples out evenly in the skillet.
Pour the egg mixture on top. Use your hands (with oven mitts on) to carefully tilt the skillet so that the eggs evenly coat the bottom. Sprinkle the gouda cheese on top. Let the eggs cook for 1-2 minutes, or just until they "set" on the bottom. Transfer the skillet to the oven and bake for 12-15 minutes or until the eggs are cooked through.
Remove from oven, cut into 6 slices, and serve immediately. Enjoy!