Instant Pot Healthy Nacho Cheese Sauce with Butternut Squash

Bowl of cheese sauce with chips

4.8 from 4 reviews

Creamy, cheesy, and good for you too!  This cheese sauce is more vegetables than it is cheese and your whole family will love it!


  • 45 cups chopped butternut squash or 1 small to medium whole butternut squash
  • 3 tablespoons butter
  • ¼ cup chopped onion
  • 2 cloves garlic
  • 4 tablespoons whole wheat flour (can substitute white flour)
  • 2 cups skim milk (or any milk you like)
  • 1 ½ cups shredded extra sharp cheddar cheese
  • ½ cup nutritional yeast (can omit, but it adds a great “cheesy” flavor)
  • 46 pickled jalapeno slices (add more or less to adjust heat – I use 8)
  • 3 tablespoons liquid from jalapeno jar
  • 1 tablespoon dijon mustard
  • 2 teaspoons kosher salt
  • 1 teaspoon cumin
  • 1 teaspoon paprika
  • 1 teaspoon chili powder


  1. Add 1 cup of water to the pressure cooker pot and place collapsible steamer basket inside.  Place chopped squash on top. Secure the lid and turn pressure release knob to a sealed position.  Cook at high pressure for 8 minutes. If using a whole squash, place the squash on top of a trivet and cook at high pressure for 25 minutes.  
  2. For chopped butternut squash, when cooking is complete, use a quick release.  For whole squash, use a natural release for 10 minutes and then release any remaining pressure (could also use a full natural release).  Remove the peel with a knife or vegetable peeler, scrape out seeds, and coarsely chop.
  3. This step can be done on the stove top while the squash is cooking or directly in the pressure cooker pot while the squash cools.  Add butter to medium saute pan on stove top or to pressure cooker pot and melt over medium high heat. Add onion and garlic and stir until softened, about 4 minutes.  Sprinkle flour on top of onions and stir for 1 minute. Slowly pour in milk, whisking constantly until it thickens, 2-3 minutes. Pour mixture into a blender and add cooked butternut squash, cheese, nutritional yeast, jalapeno slices and liquid, mustard, salt, cumin, paprika, and chili powder.  Blend until smooth.
  4. Use immediately or store in an airtight container in the fridge for up to 2 weeks.  Freezes well.


  • Use EXTRA sharp cheddar for max cheesy flavor
  • Use Bob’s Red Mill Nutritional Yeast.  It gives the sauce an amazing cheesy, nutty taste
  • Leftovers can be frozen.  I like to freeze it in pint size jars and then let it thaw overnight in the fridge, before using.  The sauce is a bit thinner after being frozen, but still plenty thick for nachos
  • Use leftovers over cooked pasta for a quick mac and cheese, as a substitute for pizza sauce (YUM!), poured over roasted veggies, drizzled on top of chili…I could go on forever!
  • To make this a Vegan Cheese Sauce: substitute butter with vegan butter, milk with almond or cashew milk, omit the cheddar cheese, and add an extra 1/4 cup nutritional yeast

Keywords: instant pot recipe, butternut squash, healthy cheese sauce