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Home » Recipes » Baking

Pumpkin Seed Cookies (Healthy & Chewy)

Updated: Mar 23, 2025 · Published: Oct 9, 2024 by Danika Vanderpyl · This post may contain affiliate links · 2 Comments

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Let's make these chewy pumpkin seed cookies with whole wheat flour! They are incredibly delicious with pumpkin pie spices, and orange zest.

Cookies are one of my favourite things to bake, I've been altering cookie recipes to add nutrient-dense ingredients for over 15 years! You are gonna love this recipe. Next, try my breakfast cookies!!

Light brown cookies with pumpkin seeds and sea salt on top.

Vision + Recipe testing

I had a vision for these cookies when I was lying in my sleeping bag on a camping trip, I was dreaming of a soft and chewy fall spice cookie! It's like a gingersnap cookie with crunchy pumpkin seeds and orange notes! It took me 8 tries to create this recipe.

First I added too many eggs and not enough oil making these cookies too doughy and tough, I didn't want that! I also tried making these cookies with pumpkin puree, but it made the cookies cakey! Now this recipe features whole wheat flour, no oats, and orange zest! I am so proud of this recipe and happy to share it with you!

Jump to:
  • Vision + Recipe testing
  • Notes about the ingredients needed
  • How to make pumpkin seed cookies with orange
  • Top tips for pumpkin seed cookies
  • Optional add in's
  • Other homemade snacks to make
  • Pumpkin Seed Cookies
  • Danika Vanderpyl, C.H.N

Notes about the ingredients needed

Here are the ingredients you need to make this fall cookie recipe, read the notes below for details.

Pumpkin seed cookie ingredients measured out and labeled, including pepitas, pumpkin puree, egg, cane sugar, coconut sugar, pumpkin pie spice, whole wheat flour, oil, vanilla.
  • Pumpkin seeds (pepitas): This is not a raw pumpkin seed recipe, it uses raw pumpkin seeds but we roast them. However, you can also use roasted and salted pumpkin seeds (the popular ones from Costco) - just skip the roasting step.
  • Orange zest: Look for an organic orange as oranges can be heavily sprayed and we want to avoid using those oranges. Alternatively, use 1 tablespoon of orange juice concentrate or a drop of orange extract.
  • Coconut sugar: I love the taste of coconut sugar, however brown sugar works perfectly too.
  • Cane sugar: You can use cane sugar or white sugar to sweeten the cookies.
  • Oil: I use grapeseed oil, however coconut oil, or organic cold-pressed canola would also be great options as they are mild-tasting oil. I haven't tested this recipe with butter but I can't see why melted butter wouldn't work.
  • Whole wheat flour: I always remember one of my reading materials in my nutrition schooling explaining how so much nutrition is stripped away when whole wheat flour is made into white flour, I was shocked. Now I try to use whole grains or whole wheat flour when possible.
  • Pumpkin pie spice: These spices bring out the flavor in these cookies. Here's my recipe to make your own affordable spice mix. Alternatively, just use cinnamon!
  • Molasses: These cookies just have a touch of molasses to reflect a pumpkin spice ginger cookie!
  • Egg
  • Baking soda
  • Sea salt

See recipe card for quantities.

How to make pumpkin seed cookies with orange

A bottle of veggie and fruit soap beside a bowl filled with water with an orange inside.

Step 1: Preheat the oven to 350 degrees Fahrenheit. Then start by washing the orange, I use a fruit and veggie wash to remove any unnatural I can from the flesh.

A zester sitting on the counter with a orange that has no more rind, and orange zest in a bowl.

Step 2: Use a zester to remove all the bright flavorful peel from the orange.

Pumpkin seeds in a cast iron frying pan.

Step 3: Place the pumpkin seeds in a frying pan over medium-high heat, stir occasionally until they start to darken or you hear popping. Then remove the pan from the heat and let it cool while preparing the cookie dough.

A mixing bowl filled with egg yolk, coconut sugar, orange zest.

Step 4: In a medium bowl place all the wet ingredients (egg, orange zest, oil, sugars, vanilla) and whisk it all together.

Flour, pumpkin pie spice, baking soda, and sea salt in a bowl.

Step 5: In a small bowl place the flour, pumpkin pie spice, sea salt, and baking soda. Use a whisk to mix everything together well.

Cookie dough in a bowl with pumpkin seeds in it.

Step 6: Add the flour mixture and the toasted pumpkin seeds to the wet ingredients, and stir until a dough forms, even using your hands. Roll into tablespoon-sized balls and place on a cookie sheet. Bake in the preheated oven 7-9 minutes until they look puffy. Take them out of the oven and let them cool on the pan for 5 minutes, this will make them the perfect texture.

Top tips for pumpkin seed cookies

Don't overbake these whole wheat orange cookies! Take them out of the oven when they look puffy and soft - this is 8 minutes for my oven. Let the cookies continue to bake on the hot cookie sheet out of the oven for 10 minutes before removing them from the pan. This will create the perfect soft and chewy cookie.

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Optional add in's

Here are some ideas to change up these pumpkin seed cookies!

  • Chocolate chips: Add ⅓ cup chocolate chips when mixing in the pumpkin seeds.
  • Dried cranberries: Add ⅓ cup of these red berries when adding the pumpkin seeds.
  • Roll cookies in cane sugar to make a similar cookie to ginger snaps!
Light brown cookies with pumpkin seeds on top and an orange behind it.

Other homemade snacks to make

Love pumpkin seeds? Or into seed cycling? Try these pumpkin seed granola bars!

  • A bite out of a chocolate energy balls with specs of ground oatmeal and a flecks of dried rose.
    Banana Chocolate Balls
  • Light brown energy ball with flecks of dates and oats, sitting on red and green apples.
    Apple Cinnamon Bites
  • A brown moist bar with pieces of oats and chocolate chips visible stacked on two other bars with a bite out of the top protein bar.
    Banana Oat Protein Bars
  • Light brown oatmeal apple cookies on a parchment paper on a plate with an apple beside it.
    Apple Oatmeal Raisin Cookies

Did you make these fall cookies with pumpkin seeds? 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. <3

Light brown cookies with pumpkin seeds on top, stacked on more cookies.

Pumpkin Seed Cookies

Danika Vanderpyl
The most INCREDIBLE autumn cookie with pumpkin pie spice, brown sugar, and pumpkin seeds. These soft and chewy cookies are easy to make and are perfect for thanksgiving or the best fall snack!
5 from 1 vote
Print Recipe Pin Recipe
Prep Time 20 minutes mins
Cook Time 8 minutes mins
Total Time 28 minutes mins
Course Dessert, Snack
Cuisine American
Servings 20 cookies
Calories 126 kcal

Equipment

  • 1 mixing bowl

Ingredients
  

  • ⅓ cup raw pumpkin seeds (pepitas)

Dry Ingredients

  • 2 cups whole wheat flour
  • 2 teaspoons baking soda
  • 1 tablespoon pumpkin pie spice or cinnamon
  • ½ teaspoon salt

Wet Ingredients

  • ½ cup + 2 tablespoon oil olive, grapeseed or coconut or organic cold pressed canola
  • ½ cup cane sugar or white sugar
  • ½ cup coconut sugar or brown sugar
  • 2 teaspoon molasses
  • 1 egg* room temperature
  • 1 orange zested*

Instructions
 

  • Preheat + zest: Preheat the oven to 350 degrees Fahrenheit. Then wash the orange and use a zester to remove the peel from the whole orange, set aside for later.
  • Roast seeds: Start by putting the pumpkin seeds in a frying pan and placing them over high heat on the stove for 3-5 minutes until they change to a darker color or start to pop. Remove the frying pan from the heat and let them cool slightly while making the cookie dough. Set aside a small handful of seeds to put on top of the cookies before baking.
  • Wet ingredients: In a large mixing bowl place the oil, white and brown sugar, molasses, egg, and orange zest. Mix until everything is glossy and smooth.
  • Dry ingredients: In a medium bowl place the whole wheat flour, baking soda, pumpkin pie spice, and salt. Whisk everything together until well combined. Dump the flour mixture and pumpkin seeds, into the wet ingredients. Mix together, even using your hands, until a thick dough forms.
  • Form cookies + bake: Use an ice cream scoop or tablespoon to make cookie balls, and place them on a lined cookie sheet. Take the pumpkin seeds previously put aside and press a few into each cookie.
    Bake the cookies at 350 Fahrenheit for 8 minutes, they will look puffy and not fully cooked, let them cool on the cookie sheet for 10 minutes to get a soft chewy texture.

Notes

Scroll up to the blog post for step-by-step photos. 
Pumpkin seeds: If you have pumpkin seeds that are roasted and/or salted, these work fine, too! Just skip the roasting step, and skip adding the salt to these cookies.
Orange zest: Use an organic orange to ensure it has not been heavily sprayed, and use a fruit wash to clean the orange before zesting it. Alternatively, use 1 tablespoon of orange juice concentrate. 
Room temperature egg: To make your egg room temperature quickly, place the egg in very warm water for 5-10 minutes. This will make the batter mix into a smooth texture and make the cookies rise evenly. 
Storing cookies: Keep these cookies in a sealing container for up to 5 days at room temperature. These cookies keep well in the freezer for up to 6 months in a sealed bag or container. 
 

Nutrition

Calories: 126kcalCarbohydrates: 18gProtein: 2gFat: 6gSaturated Fat: 1gPolyunsaturated Fat: 4gMonounsaturated Fat: 1gCholesterol: 9mgSodium: 179mgPotassium: 62mgFiber: 1gSugar: 8gVitamin A: 17IUVitamin C: 1mgCalcium: 10mgIron: 1mg
Keyword Chewy cookies, Cookies, Pumpkin Seeds, Whole wheat cookies
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. Erik says

    November 20, 2024 at 9:34 am

    5 stars
    I made these last week and they were a hit! Love the citrus flavour with the seedy crunch and the depth the molasses brings. I need to make another batch ASAP!

    Reply
    • Danika Vanderpyl says

      November 22, 2024 at 7:10 am

      Thanks for sharing Erik! So glad you made these, I love the hints of orange too!

      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!

About me

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