Add the chopped bacon to a large skillet or saucepan over medium heat. Cook until the bacon is lightly browned and slightly crisp. Carefully drain most of the excess bacon fat, reserving about 1 tablespoon in the pan with the bacon.
Return the pan to low heat and add the diced shallots and minced garlic and cook for about 10 minutes, stirring occasionally, until softened and deeply caramelized.
Stir in the thyme sprigs. Cook for about 1 minute, just until fragrant.
Add the dark brown sugar, maple syrup, apple cider vinegar, and a pinch of kosher salt. Stir well to combine.
Bring the mixture to a gentle simmer. Cook uncovered over low to medium-low heat for 15–20 minutes, stirring occasionally, until the liquid has reduced and the mixture is thick and glossy. Do not cook it until completely dry. The bacon jam will thicken more as it cools.
Remove about ⅓ of the jam (without the thyme stems) and use an immersion blender to puree it. Return to the pan, stir well, and simmer 1-2 more minutes. (This step is optional, but I highly recommend it).
Remove the thyme stems and stir everything together. Transfer the bacon jam to a heat-safe container and allow it to cool. The jam will thicken as it cools.