Heat a large stockpot over medium heat. Add 3 T. neutral cooking oil (I used grapeseed oil). Add vegetables and garlic. Sprinkle spices and salt on top of vegetables. Mix around with a wooden spoon, being careful not to let it burn. Sauté until soft and slightly brown, about 15 minutes, lowering heat if you need. Add a little more oil if it starts sticking too much to the bottom.
Raise heat to medium-high. Add ground beef. Break up meat with a wooden spoon until no pink remains, about 8-10 minutes.
Add crushed and diced tomatoes, chicken stock, kidney beans, and pinto beans. Add the chopped up chipotle peppers in adobe sauce. Mix and bring to a boil.
Lower heat and simmer with lid partly on/off. Stir once in awhile so it doesn’t stick to the bottom of the pot. Simmer for about 30 minutes, on low heat, until the color deepens to a darker red.
Make the Masa flour slurry. Mix the Masa flour and water in a small bowl. Mix well until there are no clumps. Simmer for 5-10 minutes more.
Taste and adjust seasonings with more salt and pepper, if needed. Serve with avocado, grated cheese, sour cream, cilantro, green onions, etc. I also like to serve tortilla chips, Fritos, or cornbread on the side.