Preheat your oven to 375°F (190°C) and line a standard 12-cup muffin tin with paper liners or generously coat with non-stick spray.
In a large skillet over medium heat, cook bacon strips until crispy. Transfer to paper towels to drain excess grease, then crumble or chop finely. Reserve 1 tablespoon of bacon fat for extra flavor.
Peel and dice the apples into small, uniform 1/4-inch cubes.
In a large mixing bowl, whisk together flour, baking powder, salt, pepper, and garlic powder.
In a separate bowl, whisk together eggs, milk, oil or melted butter, and maple syrup until fully incorporated.
Make a well in the center of your dry ingredients and pour in the wet mixture. Use a spatula to fold together using no more than ten folds to prevent overworking the gluten.
Gently fold in the crumbled bacon, shredded cheese, diced apples, thyme leaves, and green onions. Reserve a small amount of bacon, cheese, and apple pieces to sprinkle on top of the muffins.
Using an ice cream scoop or large spoon, divide the batter evenly among the prepared muffin cups, filling each about 3/4 full. Top with reserved bacon, cheese, and apple pieces.
Bake in the preheated oven for 22-25 minutes, or until a toothpick inserted into the center comes out clean with a few moist crumbs. Rotate the pan halfway through baking for even coloring.
Allow muffins to cool in the pan for 5 minutes before transferring to a wire rack to cool completely. Serving them slightly warm maximizes the flavor experience.