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Home » Recipes » Baking

Pumpkin Seed Muffins (with Whole Wheat Flour)

Updated: Jul 25, 2025 · Published: Oct 19, 2024 by Danika Vanderpyl · This post may contain affiliate links · 1 Comment

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These breakfast pumpkin seed muffins are mouthwatering! Each bite is a perfect balance of fluffy, moist muffin and the satisfying crunch of toasted pumpkin seeds among the oats, whole wheat flour, and canned pumpkin.

I'm all about wholesome muffins over here; I've been baking muffins for more than 15 years. Next, try my blueberry muffins or these fall apple chocolate chip muffins!

A orange pumpkin muffins with flecks on green pumpkin seed in it, sitting on a bowl of pumpkin seeds.

Why you'll love these muffins:

  • They're nutrient dense pumpkin muffins with pumpkin seeds and oatmeal - each muffin contains 4 grams of protein.
  • Made with pumpkin seeds to support cycle syncing in the follicular phase. Read more about this here.
  • These pumpkin muffins are made with oil, making them naturally dairy-free (no yogurt, no butter).
Jump to:
  • Why you'll love these muffins:
  • Ingredients needed for pumpkin seed muffins
  • How to make whole wheat pumpkin muffins
  • Muffin liners
  • Top muffin tips
  • Variations and add in's
  • For a complete snack eat these muffins with
  • Other pumpkin seed recipes
  • Pumpkin Seed Muffins with Whole Wheat Flour
  • Danika Vanderpyl, C.H.N

Ingredients needed for pumpkin seed muffins

Ingredients in bowls for pumpkin muffins with labels on them.
  • Pumpkin seeds (pepitas): I use raw pumpkin seeds, however roasted would work fine too (and if they are salted...still use them, just don't add any additional salt). I get my pumpkin seeds from organic matters, amazon, or a bulk grocer. They are also called pepitas.
  • Pumpkin puree: I used canned pumpkin puree (not pumpkin pie filling). This is a perfect recipe to use 1 cup of leftover pumpkin puree.
  • Rolled oats: I like the texture and the nutrition when adding oats to these pumpkin muffins along with the pumpkin seeds. It gives a bit of a crunch and just more texture. I used rolled oats (not quick oats).
  • Whole wheat flour: I like to use whole wheat flour in my pumpkin muffins to make them more nutrient-dense (instead of using white flour).
  • Organic cane sugar: Use cane sugar or granutated white sugar for these muffins.
  • Baking powder & baking soda: I tried to skip the baking soda but after testing it, the texture and rise is better with a little of both baking soda and baking powder.
  • Sea salt: A little sea salt increases the flavor of these wholesome muffins!
  • Oil: Any mild tasting oil can be used for these muffins, including grapeseed, organic canola, olive oil, or melted coconut oil.
  • Brown sugar: Brown sugar or coconut sugar adds a balanced flavor bringing the fall pumpkin muffin vibes all together!
  • Eggs
  • Vanilla

See recipe card for quantities.

How to make whole wheat pumpkin muffins

Oats, whole wheat flour, sea salt, in a bowl.

Step 1: Preheat the oven to 425 degrees Fahrenheit (220C). Mix the dry ingredients (whole-wheat flour, rolled oats, sea salt, baking powder, baking soda, and cane sugar) together with a whisk to incorporate well.

Eggs, pumpkin puree, vanilla, oil, in a glass mixing bowl

Step 2: In another medium mixing bowl, place the eggs, pumpkin puree, vanilla, oil, and brown sugar. Whisk until everything is thick and glossy.

Chopped pumpkin seeds, whole wheat flour, and the wet ingredients in a glass mixing bowl.

Step 3: Use a chopper or a knife to break the pumpkin seeds (pepitas) into small pieces. Then add the chopped seeds and the flour mixture to the wet mixture of pumpkin puree and eggs. Use a spatula to stir about 12-15 times; there may be a few small flour streaks and this is okay.

Pumpkin muffin batter in silicone muffin cups in a muffin tray.

Step 4: Place the muffin liners into a muffin tray. Add just less than ⅓ cup batter into each muffin cup. Then top with a few whole pumpkin seeds.

Bake the whole-wheat pumpkin muffins at 425 degrees Fahrenheit (220C) for 7 minutes, then turn the oven down to 375 degrees Fahrenheit (190C) and bake for another 7-8 minutes. Remove muffins from the oven when they spring back from touch and when the center does not look gooey.

Muffin liners

I use silicone muffin cups to lessen the cleanup, I'd rather wash those than scrub the muffin pan! If you don't have muffin liners, grease the pan well and watch the oven as muffins can cook faster without liners (especially the silicone ones).

Top muffin tips

For a nice dome muffin we want a thick batter, with baking powder and baking soda.

So that the breakfast pumpkin muffins turn out light and fluffy, and not dense, only stir the batter just until it's mixed, about 12-15 folds, there may be a few flour streaks - that's okay, but do not overmix the batter.

Start the oven at 425 degrees Fahrenheit (220C) - this high temperature will insure the muffins rise, then turning the oven down to 375 degrees Fahrenheit (190C) will cook the muffin through without drying them out.

Variations and add in's

Boost these muffins with all your favorite things!

  • Flax seeds: Add 2 tablespoons of flax to increase healthy fats. An increase of flax seeds and pumpkin seeds in the first half of your cycle (first twoish weeks) as a women can support your hormone health.
  • Chocolate chips: Add ⅓ chocolate chips to the muffin batter for healthy pumpkin chocolate chip muffins!
  • Ginger powder: I was tempted to add ginger powder to these muffins like my carrot pineapple muffins...but I'm leaving it as an option for you to decide! Add 1 teaspoon of powdered ginger to the dry ingredients if you desire.
  • Pumpkin pie spice: Make these pumpkin seed muffins with all the cozy fall vibes, add 1 teaspoon of pumpkin pie spice (here's my recipe to make your own spice blend!).

For a complete snack eat these muffins with

These muffins do have a good amount of fiber and protein, making your blood sugar more balanced and keeping you full longer, however enjoy the following ideas to eat along with your muffin:

  • pumpkin seed butter or almond butter spread on top of the halves
  • a handful of nuts
  • enjoy with a glass of milk (like organic soy milk which my kids are loving these days!)
  • a piece of cheese (my husbands favorite)
Dark orange colored muffins with green pepitas on top.

Other pumpkin seed recipes

Do you have leftover pumpkin puree? Make this pumpkin snack cake!

  • A flat lay photo of a dark red smoothie with hemp hearts, cherries, strawberries, and raspberries on top.
    Smoothie for Your Period
  • Light brown energy bites with flecks of oats and dark chocolate chips with pumpkin seed on top and cinnamon sticks beside it.
    The Best Pumpkin Spice Oatmeal Balls
  • A piece of sourdough with green pumpkin seed butter on top with a sprinkle of cinnamon sitting on a pottery plate.
    Simple Pumpkin Seed Butter Recipe (Nut-Free & Vegan)
  • A close up of yellow hummus with chickpeas, pumpkin seeds, paprika, and sea salt.
    Pumpkin Seed Hummus (savory)

Did you make these pumpkin seed muffins? Would you take 5 seconds to give a star rating and review just below the recipe? That means a lot to me and helps the growth of Beside the Mountain blog.

A pumpkin colored muffin with pumpkin seeds on top and sitting in a dish of olive green pumpkin seeds.

Pumpkin Seed Muffins with Whole Wheat Flour

Danika Vanderpyl
A healthy whole wheat pumpkin muffin with pepitas and oats. These are a perfect wholesome snack; you are gonna love these moist muffins!
5 from 1 vote
Print Recipe Pin Recipe
Prep Time 20 minutes mins
Cook Time 16 minutes mins
Total Time 36 minutes mins
Course Breakfast, Snack
Cuisine American
Servings 12 muffins
Calories 178 kcal

Equipment

  • 1 muffin pan
  • 12 silicone muffin cups

Ingredients
  

Dry ingredients

  • 1 ⅓ cups whole wheat flour
  • ⅓ cup rolled oats
  • ½ cups organic cane sugar
  • 2 teaspoons baking powder
  • ½ teaspoon baking soda
  • ½ teaspoon salt

Wet ingredients

  • 2 eggs
  • 1 cup pumpkin puree
  • 2 teaspoon vanilla
  • ⅓ cup oil (grapeseed, organic canola, olive oil, or melted coconut oil)
  • 3 tablespoon brown sugar

Add later

  • ⅓ cups pumpkin seeds chopped + a few for the top

Instructions
 

  • Preheat the oven to 425 degrees Fahrenheit (220C).
  • Mix dry ingredients: In a large bowl mix the dry ingredients - flour, oats, sugar, baking powder, baking soda, and salt. Use a whisk to mix everything well.
  • Mix wet ingredients: In a medium mixing bowl, place the eggs, pumpkin puree, vanilla, oil, and brown sugar. Whisk together until it is well combined.
  • Fold everything together: Chop the pumpkin seeds with a chopper or a knife until they are little chunks. Add the pumpkin seeds and flour mixture into the wet ingredients. Use a spatula to stir the batter together, about 12-15 folds, just until everything is incorporated. Do not over-stir.
  • Scoop & bake: Place silicone liners or paper liners into a muffin pan. Add a little less than ⅓ cup of batter to fill each muffin cup. Place the muffin tin in the preheated oven (425 degrees Fahrenheit or 220C) to bake for 7 minutes, then turn the oven down to 375 degrees Fahrenheit (190C) and bake for another 7-8 minutes. Remove muffins from the oven when they spring back from the touch and when the center does not look gooey.

Notes

Muffin storage: Store the breakfast pumpkin muffins in a container lined with a paper towel for up to 5 days at room temperature. If you want them to last longer, I recommend freezing them and taking them out as desired. Read more about freezing muffins and storing muffins here.
For step by step photos, scroll up to the blog post.
For optional add-ins, see the blog post above! 

Nutrition

Serving: 1muffinCalories: 178kcalCarbohydrates: 25gProtein: 4gFat: 8gSaturated Fat: 1gPolyunsaturated Fat: 2gMonounsaturated Fat: 5gTrans Fat: 0.03gCholesterol: 27mgSodium: 226mgPotassium: 131mgFiber: 2gSugar: 12gVitamin A: 3219IUVitamin C: 1mgCalcium: 58mgIron: 1mg
Keyword Fall Snacks, Healthy Muffins, Pepitas, Pumpkin Puree, Pumpkin Seeds, Whole wheat muffins
Did you love this recipe?Make sure to leave a comment below!
danika sitting in a chair

Danika Vanderpyl, C.H.N

I create snack recipes with healthy ingredients that are mostly already in your kitchen. I'm certified in Holistic Nutrition and I care about giving my kids real food. Let me share my nutrient-dense easy snacks with you.

Learn more about me →

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Comments

    5 from 1 vote

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    Recipe Rating




  1. Becky says

    October 30, 2025 at 4:39 pm

    5 stars
    A great fall treat!

    Reply
Danika-vanderpyl-hiking-with-mountains

Hey hey! I'm Danika.

I'm certified in holistic nutrition and I create snack recipes! Because unprocessed, wholesome, nutrient-dense snacks are hard to find but I want everyone to know they are easy to make!

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