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How to Clean Pumpkin Seeds

How to clean pumpkin seeds so they are crispy when you bake or make air fryer pumpkin seeds to perfection! Homemade toasted pumpkin seeds are the best during the Fall. 

how to clean pumpkin seeds

We love homemade pumpkin seeds once Fall arrives. The bagged ones just aren’t the same! Here’s how to clean pumpkin seeds so once you bake them they’re as crispy as possible, just the way you want them. 😉 (affiliate links present)

Pumpkin Seed Recipe

  • Pumpkins are kinda’ messy fellas, but boy do they make tasty goodies! 

I will of course not just share with you how to cut, separate the goo and clean these bits, but also how to roast and cook this healthy snack. You can use the same method to make roasted spaghetti squash seeds too. Any squash will do. 😉

Do you usually just throw away all that goop WITH the seeds stuck in it?? STOP!! You’re missing out on some wholesome snacks. With a bit of butter and seasoned salt they may become your favorite part of this gourd.

cleaning a pumpkin

How to Clean Pumpkin Seeds

  • First you need to pick our your favorite one. Whether it comes from a pumpkin patch, or grocery store like ours did it doesn’t matter.
  • When you’re ready to carve your pumpkin get out a large bowl.
  • Once the top (or bottom is the way we do it many times) is off it’s time to scoop!

Cleaning pumpkin seeds

This is what you’re going to need to get started;

  1. Large bowl
  2. Small bowl
  3. A few paper towels, or a third bowl for the trash
  4. Spoon that is large and strong for scooping
  5. Running water like a kitchen sink
  6. Colander
  7. Small pot and sea salt if you want to boil them, we will get to that later
  8. How Long to Cook Pumpkin Seeds is here in a number of different ways
    • Baking sheet if you’re using your oven to cook them

Or if you’re using your hot air machine and/or Ninja Foodi there is a link to those directions at the top of this post for you.

pumpkin seeds

Use your spoon to scrape the gunk and a bit of the inside of the pumpkin out. The top layer where the yuck is connected is best to remove in order to preserve pumpkins longer.

  • You don’t want it to start decaying right after you carve it, your kids will be REALLY upset.

What do you spray on pumpkins to make them last longer?

Pumpkins shrivel up because they run out of moisture. Spraying it every day with water mixed with a few drops of bleach will keep it moist and ward off bacteria. 

How do you keep pumpkins from rotting outside?

Vaseline is a great way to keep your carved pumpkins from drying out and getting that wrinkly look. It’s water-repellant, so it seals in the natural moisture while keeping outside moisture away. Spread the petroleum jelly inside your pumpkin and around all of the cut out areas.

cleaning pumpkin seeds

This is where the bowls come into play. You can use a few folded up paper towels too for what you’re going to throw away.

Best way to separate the seeds from this is to grab a chunk with one hand and squeeze the seeds off the end one or a few at a time.

  • I will admit this is a tedious process. I tend to do a few pumpkins all at the same time so I can make a large batch of toasted pumpkin seeds. Just do it all at once I say.

How to Boil Pumpkin Seeds

But they are still gross!!! I know. There are 2 ways of how to clean pumpkin seeds well. I use the second boiling method when I roast pumpkin seeds in the oven, but not when I’m air frying them.

boiling pumpkin seeds
clean pumpkin seeds
  • Rinsing them off is really the best method so they aren’t cooked until you put them into your air fryer or convection oven, but that is up to you.
  • Some people are totally grossed out by pumpkin pulp and want ALL of the bits off. A quick bath in boiling water will solve that.

What is the benefit of eating pumpkin seeds?

Like nuts, pumpkin seeds are a great source of protein and unsaturated fats, including omega-3. They also contain a good amount of nutrients including iron, selenium, calcium, B vitamins and beta-carotene, which the body converts into vitamin A. They’re naturally gluten free too.

making pumpkin seeds

Can I eat pumpkin seeds in the shell?

Yes!! I think they’re best this way. The actual pumpkin seed is actually dark green, flat, mildly sweet and tender, like the seeds of other kinds of winter squash. Most pumpkin seeds are encased in a cream-colored shell, or hull, that is just as edible as the kernel it protects.

How to Roast Pumpkin Seeds

There is a link at the top of this post as to how to crisp these in your air fryer, we love that method. Follow our roasted homemade pumpkin seeds in the oven for that way.

Are pumpkin seeds good for Keto?

They are in fact low in carbs, making them ideal for low carb diets and keto diets. They are also high in vitamins and minerals like zinc, magnesium, manganese and fiber. All in all they’re great for digestive health.

toasted pumpkin seeds

What is the best way to eat pumpkin seeds?

You can eat pumpkin seeds raw or cooked, depending on your preference. If you eat them raw, clean them this way first. Then eat them with the shell or break it off with your teeth and spit it out like you would with a sunflower seed.

What can you do with pumpkin

how to clean pumpkin seeds

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how to clean pumpkin seeds
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How to Clean Pumpkin Seeds

Course Snack
Cuisine American
Keyword pumpkin seeds
Prep Time 15 minutes
Cook Time 25 minutes
Servings 4
Calories 126kcal
Author The Typical Mom


  • 1 pot
  • 1 Spoon
  • paper towels



  • Use a sharp knife to cut the top of the pumpkin off, large enough to scrape out the inside, or in half.
  • Use your hands or a spoon to scoop out the seeds on the inside. Pour seeds into a colander. Rinse the seeds under the sink with water. Pick out the seeds and pulp, separating the two and discard the pieces you don't want. Spread the seeds on several paper towels, pat to dry and you have clean seeds.
  • If you want to proceed to bake them to crispy snacks you'll want to put them into a pot of boiling salted water. Keep them inside this on a consistent rolling boil for about 3 minutes or until your seeds float. Use a slotted spoon to get them out.
  • Lay out some new, dry, paper towels and pour them on top. Press down to absorb the excess moisture. To get them as crispy as possible you want them as dry as much possible. Ideally let them sit overnight but a minimum of 4 hours.
  • Once dried pour them into a bowl and toss with olive oil or melted butter and seasonings, toss to coat. If you want to bake them, pour on to a non stick baking sheet. Preheat oven to 350 degrees F. Roast for about 20 minutes flipping them over halfway until crispy. Allow to cool completely before enjoying so they can continue to get crispy as they dry.
Nutrition Facts
How to Clean Pumpkin Seeds
Amount Per Serving (1 oz)
Calories 126 Calories from Fat 45
% Daily Value*
Fat 5g8%
Saturated Fat 3g19%
Trans Fat 0.2g
Polyunsaturated Fat 0.2g
Monounsaturated Fat 1g
Cholesterol 11mg4%
Sodium 37mg2%
Potassium 1157mg33%
Carbohydrates 22g7%
Fiber 2g8%
Sugar 9g10%
Protein 3g6%
Vitamin A 29075IU582%
Vitamin C 31mg38%
Calcium 73mg7%
Iron 3mg17%
* Percent Daily Values are based on a 2000 calorie diet.
Recipe Rating

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Tuesday 26th of October 2021

Please don't spray them with bleach!!! It will kill the animals that munch on them outside!

Chemical Engineer

Saturday 22nd of October 2022

@Sin, Not true. "Concentrated" bleach will kill animals. Diluted forms of sodium hypochlorite will burn of the chemicals far too quickly for an animal to ingest any lethal dose. This is the reason even as a human you're told to dilute the chemical. Nobody is just dumping straight bleach into a pumpkin.

Chemical Engineer

Saturday 22nd of October 2022


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