Combine 1 tbsp brown sugar, coffee, cocoa, chili powder, paprika, salt, onion powder, salt, pepper, garlic powder, cumin, and oregano in a small bowl. Place chunks of beef into a zip lock bag and add mixed spices. Shake to evenly combine.
Heat olive oil over medium-high heat in large skillet or cast iron pan. Add pieces of chuck roast (in batches to not overcrowd) and cook 2-3 min per side until browned. Place in bottom of crockpot.
Turn heat down to medium-low and add diced onions, cooking 3-4 minutes until slightly softened. Add beer and stir with wooden spoon to scrape up all those brown bits on the bottom of the pan. Add onions and beer to crockpot.
Add tomatoes, beans, sweet potatoes, chipotle pepper, remaining 1 tbsp of brown sugar and apple cider vinegar to the crockpot.
Give everything a stir to combine, cover and cook on low for 8-10 hours or until the meat is fall-apart tender.
Serve with diced onions, shredded cheese and sour cream if desired.