In a large skillet over medium heat, add the olive oil. Once hot, add the diced yellow onion and jalapeño. Sauté for 3-5 minutes until softened and fragrant.
Add the ground beef to the skillet. Cook until browned and fully cooked through, breaking it up with a wooden spoon as it cooks, about 6-8 minutes. Drain excess fat if necessary.
Stir in the diced chipotle peppers, chili powder, cocoa powder, kosher salt, black pepper, cumin, oregano, and smoked paprika. Mix well to combine.
Pour in the fire-roasted diced tomatoes and beef stock. Bring the mixture to a simmer and cook for about 10 minutes, allowing the flavors to meld.
In a separate skillet, heat the vegetable oil over medium heat. Lightly fry each corn tortilla for about 30 seconds on each side until pliable. Drain on paper towels.
Preheat your oven to 350°F (175°C). Spread a thin layer of the beef mixture on the bottom of a baking dish. Take a tortilla, fill it with a few spoonfuls of the beef mixture, and roll it up tightly. Place seam-side down in the baking dish. Repeat with remaining tortillas and filling.
Once all the enchiladas are in the dish, pour any remaining beef mixture over the top and sprinkle with shredded cheese.
Cover the baking dish with aluminum foil and bake in the preheated oven for 20 minutes. Remove the foil and bake for an additional 10-15 minutes until the cheese is bubbly and golden.
Remove from the oven and let cool for a few minutes. Top with minced yellow onion and cilantro before serving. Enjoy your Chipotle Ground Beef Enchiladas!