Preheat the oven to 400°F (200°C).
In a large, deep skillet over medium heat, cook the chopped bacon until crispy. Use a slotted spoon to transfer the bacon to a plate, reserving the bacon grease in the skillet.
Bring a large saucepan of water to a boil. Add the cauliflower florets and cook for 5 minutes. Drain and set aside.
Add olive oil to the reserved bacon grease in the skillet. Stir in the diced onion and minced garlic, sautéing for 3–5 minutes until the onion becomes tender and translucent.
In a bowl, whisk together the milk and flour until smooth. Gradually pour this mixture into the skillet. Bring it to a gentle boil, stirring occasionally, until small bubbles form around the edges.
Stir in the shredded cheddar cheese, parmesan cheese, and salt. Continue whisking until the cheese sauce is smooth and creamy.
Remove the skillet from the heat and fold in the cooked cauliflower, ensuring every floret is evenly coated in the cheese sauce.
Transfer the cheesy cauliflower mixture to an 8x8-inch baking dish. Evenly sprinkle the cooked bacon over the top.
Place the baking dish in the oven and bake for 20 minutes.
Remove from the oven, garnish with chopped chives, and serve warm.