Put mayocoba beans into a large container with enough cool water to cover by several inches. Let beans soak 8 hours to overnight.

Drain mayocoba beans and rinse thoroughly; put into a large stockpot. Pour enough water into the pot to cover beans by a few inches; bring to a boil, reduce heat to medium-low and place a cover on the pot, and cook at a simmer until beans are soft in the center, about 90 minutes.

While the beans simmer, heat oil in a large skillet over medium heat. Cook and stir onion in hot oil until tender, about 5 minutes; add tomatoes and serrano pepper and simmer until the tomatoes have softened slightly, about 5 minutes. Reduce heat to medium-low and continue cooking until the liquid begins to thicken, about 10 minutes more. Remove from heat.

Cook and stir bacon in a large, deep skillet over medium-high heat until very crispy, about 10 minutes; remove bacon from skillet with a slotted spoon and drain on a plate lined with paper towel.

Cook ham cubes in the bacon fat in the skillet until browned, about 5 minutes; remove with slotted spoon to the plate with the bacon to drain.

Once the beans have cooked, stir the tomato mixture, bacon, ham, beer, jalapeno peppers, cilantro, and chicken bouillon granules into the beans; season with sea salt. Bring the mixture to a simmer and cook until the beans are completely softened, about 30 minutes.