Preheat oven to 180 degrees C. Grease a 20x30cm baking dish.
Heat the olive oil in a large frypan over medium heat and cook the onion and garlic until the onion is translucent, about 5 minutes. Stir in the zucchini, pumpkin and red capsicum. Cook, stirring frequently, until the zucchini and pumpkin are tender, about 10 minutes. Stir in the black beans, green salsa, cumin and cayenne pepper. Cook and stir the filling until it thickens, 5 to 8 more minutes.
Divide 250g cheese among the tortillas. Spoon zucchini-pumpkin filling into each tortilla, over the cheese, in a line down the centre. Roll up the tortillas and place them into the prepared baking dish with the seam sides down.
Bake in the preheated oven until the cheese is melted and the tortillas are heated through, about 15 minutes. Sprinkle the rest of the grated cheese over the tortillas before serving.