This recipe doesn't make sticky-sweet brown sugar baked beans. Think of them like the top crust of a good cassoulet.
- 2 cups dried navy or cannellini beans, soaked overnight
- 2 medium onions, 1 halved, 1 thinly sliced
- 1 Parmesan rind (optional), plus ½ cup finely grated Parmesan
- 1 head garlic, halved crosswise, plus 4 cloves, finely chopped, divided
- 2 teaspoons kosher salt, plus more
- 8 ounces slab bacon, cut into 2x¼” pieces
- 1 large shallot, thinly sliced
- 4 sprigs thyme plus 1 tablespoon leaves
- Freshly ground black pepper
- 1½ cups coarsely torn fresh breadcrumbs
Drain beans and place in a large heavy pot along with halved onion, Parmesan rind (if using), halved head of garlic, bay leaves, and 2 tsp. salt. Add water to cover by 2”. Bring to a boil, reduce heat, and simmer until beans are tender, 1–1½ hours.
Meanwhile, cook bacon in a large skillet over medium heat, turning occasionally, until brown and most of fat has rendered, 8–10 minutes. Transfer to a plate with tongs or a slotted spoon.
Add thinly sliced onion, shallot, thyme sprigs, and three-fourths of chopped garlic to pan drippings in skillet; season with salt and pepper. Cook, stirring occasionally, until onion is starting to caramelize and is very soft, 10–15 minutes. Add wine, bring to a simmer, and cook, stirring occasionally, until liquid is almost completely evaporated, about 4 minutes. Remove from heat and pluck out thyme sprigs.
Preheat oven to 400°. Drain beans, reserving cooking liquid. Transfer beans to a large bowl and mix in bacon, onion mixture, thyme leaves, grated Parmesan, and 1½–2 cups cooking liquid (this will be most of it; mixture should be consistency of stew); season with salt and pepper. Transfer beans to a shallow 1½-qt. baking dish.
Mix breadcrumbs, oil, and remaining chopped garlic in a medium bowl; season with salt and pepper. Scatter over beans; bake until liquid is thickened and bubbling and crumbs are golden brown, 45–55 minutes. Let cool slightly before serving.
Do Ahead: Beans can be baked 5 days ahead. Let cool; cover and chill.