Before chopping the blossoms, check for any bugs inside. Wash each blossom throughly with water.
Remove the stems and roughly chop the blossoms.
In a medium pan, heat 1 tbsp of oil on a medium high heat. Once oil it hot, saute the onions for 5 minutes.
Stir in the peppers and garlic and cook for another minute.
Add chopped blossoms along with salt and few grinds of pepper, toss to coat evenly with onions, garlic and pepper.
Cook until the blossoms as just wilted, around a minute. Transfer the mix into a clean bowl and let it cool completely.
Spread 1 to 1 1/2 tbsp of chipotle sauce on a corn tortilla. Spread around 2 ounce cheese on one half of the tortilla, top with squash blossom mix and fold the other side of the tortilla over. Press down gently with your hand.
Either in same medium pan or a cast iron skillet, heat 1 tsp of oil. Place the prepared quesadilla and cook for 30 seconds to a minute on each side.
Once both sides are crispy and the cheese in the quesadilla is melted, removed from pan.
Cut each quesadilla into triangles and serve with your favorite salsa.