Preheat oven to 325 degrees.
Spray a 1 quart baking dish with cooking spray. Set aside.
In a large skillet over medium/high heat, cook the cut bacon until almost crisp.
Use a slotted spoon to remove 3 tablespoons of the bacon to a plated lined with a paper towel. Set aside.
Remove all but 3 tablespoons of the bacon grease from the skillet.
Add the sliced onions, salt, pepper and garlic to the skillet with the remaining bacon, and cook, stirring occasionally, until the onions start to turn golden brown (approximately 10-15 minutes).
Reduce the heat to low and stir in the maple syrup and the all purpose flour.
Cook for an additional 1-2 minutes, stirring frequently.
Turn off the heat and stir in the shredded cheeses. Stir well to combine.
Spoon the dip into the prepared baking dish and top with the reserved partially cooked bacon and the fresh thyme leaves.
Bake in the preheated oven for 15-20 minutes.
Serve immediately with crackers, veggies, bread, or chips.
Enjoy!