Preheat the oven to 375 degrees F (190 degrees C). Grease one 9- or 10-inch Bundt pan.
Cream butter and sugar together. Add beaten egg and mix well. Stir in mashed cooked beans and vanilla.
Sift flour, baking soda, salt, cinnamon, cloves, and allspice together. Add pecans, raisins, and apple to the flour mixture. Stir to coat. Pour flour mixture into the creamed mixture and stir until just combined. Pour batter into the prepared pan.
Place pinto beans into a large bowl and cover with several inches of water; soak at least 8 hours and up to 24 hours. Drain and rinse before using.
Place soaked pinto beans, onion, garlic, and jalapeno peppers in a slow cooker; pour enough water over mixture to cover with several inches. Cook on Medium-Low, 4 to 6 hours. Season with salt and black pepper.