In a large pot, combine the soaked beans with filtered water, white onion, jalapeño and garlic for flavor.
Bring water to a simmer and simmer gently with lid tilted until desired tenderness is reached, about 45 minutes to 75 minutes. Stir occasionally and add water to cover the beans as needed.
When they are tender, add salt. Continue cooking the beans uncovered for 5-10 minutes, stirring frequently, to thicken the bean liquid. Remove the half of onion and discard. Do not drain liquid.
The homemade pinto bean recipe will leave you with leftovers. Freeze extra beans and their sauce in 2 cup portions and use for taco or grain salads, burritos, quesadillas and enchiladas.