In a large skillet over medium-high heat, cook the ground beef and diced onions together. Break the meat apart with a spatula as it cooks. Once the beef is no longer pink and the onions are translucent, add the minced garlic and cook for another minute until fragrant.
Drain any excess grease from the skillet. Stir in the taco seasoning and 1/4 cup of water. Simmer the mixture for 3 to 5 minutes until the liquid has mostly evaporated and the beef is well-coated in the sauce. Remove from heat and set aside.
Lay a flour tortilla flat on a clean surface. Sprinkle about 1/4 cup of cheese over one-half of the tortilla. Spread a generous layer of the seasoned beef over the cheese, then top with another 1/4 cup of cheese. Fold the tortilla in half to create a half-moon shape.
Preheat your air fryer to 375°F (190°C). Lightly spray the air fryer basket with cooking spray. Place one or two quesadillas in the basket, making sure they do not overlap. Spray the tops of the tortillas lightly with cooking spray. Cook for 4 to 5 minutes.
Carefully flip the quesadillas using a spatula. Cook for an additional 2 to 3 minutes, or until the tortillas are golden brown and the cheese is fully melted. Repeat with the remaining tortillas and serve warm.