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In a large pot, combine the soaked beans with filtered water, white onion, jalapeño and garlic for flavor.
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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.
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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.
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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.