Preheat an oven to 350 degrees F (175 degrees C). Grease a 12 muffin miniature muffin pan.
Heat the oil in a large skillet over medium heat. Stir in the onion and bacon. Cook until onion is translucent and bacon is browned, about 5 minutes. Stir in the carrot and zucchini; cook until they begin to soften, about 2 minutes. Transfer mixture to a bowl to cool.
Beat the eggs, cream, and Parmesan cheese together in a large bowl. Season with salt and pepper. Stir egg mixture into cooled zucchini mixture; stir in flour. Spoon the batter evenly into the prepared muffin cups.
Bake in preheated oven until a toothpick inserted in the center comes out clean, 15 to 20 minutes.