Peel and mince just 1 clove garlic. Peel and finely dice the red onion. Remove the husk from the tomatillo and rinse. Finely dice the tomatillo. Trim, deseed, and chop the green bell pepper. Halve the lime.
Add the juice from half the lime to a medium bowl. Add the minced garlic, just 2 tbsp diced onion, diced tomatillo, and a pinch of salt. Stir the tomatillo salsa to combine and chill in the refrigerator until you’re ready to serve.
Place a medium saucepan over high heat and add the remaining 2 cloves garlic, remaining diced onion, chopped bell pepper, 1 1/2 cups water, and ½ tsp salt. Bring to a boil, then reduce heat to low and simmer until the vegetables soften, about 5 to 7 minutes.
Transfer the pepper mixture to a blender. Add the juice from the remaining lime half, baby spinach, cilantro, and a pinch of salt. Blend the salsa verde until smooth.
Drain and rinse the black beans and pat dry with a paper towel. Remove the chipotle sausage from the packaging and cut into rounds. Place a large nonstick skillet over medium-high heat with 1 tbsp vegetable oil.
Once hot, add the beans and sausage and cook, shaking the pan occasionally until the sausage is crisp in places, about 4 to 5 minutes. Transfer the beans and chipotle sausage to a plate.
Cut the corn tortillas into quarters. Return the skillet to low heat (no need to rinse). Add the salsa verde and the quartered tortillas to the skillet. Flip the tortillas to evenly coat in the sauce and cook until hot, about 2 to 3 minutes.
Divide the chilaquiles between large plates. Top with black beans, chipotle sausage, and tomatillo salsa.