In a pan/skillet melt butter, add onions and jalapeños. Sauté for several minutes until onions begin to soften, add in garlic and allow to cook another minute until garlic is fragrant. Add the flour in and mix until completely combined. All to cook for another couple minutes.
Slowy add chicken broth constantly string until combined and no lumps. Add in cream cheese, milk and mix together. Bring to a slight boil reduce heat and allow add in cheddar cheese. Cook until cheese is melted and the mixture has thickened. Add in chicken and bacon, pour the mixture into a pie dish.
Cover with a thawed pie crust. Place in oven and back for 30 minutes. At 20 minutes, I added a little more cheese, bacon and jalapño and popped it back in for 10 more minutes.