Rich Chocolate Chip Pumpkin Seed Cookies

Finding the perfect cookie recipe that satisfies everyone’s cravings while sneaking in some nutrition can feel impossible. You want something sweet enough for the kids, interesting enough for adults, and maybe just a little bit healthier than your typical chocolate chip cookie – but most recipes either go too healthy and lose all the flavor, or stick with the same old combinations that get boring fast.

That’s where these chocolate chip pumpkin seed cookies come in to save the day. They give you all the comfort of a classic cookie with a fun twist that adds great texture and a subtle nutty flavor, plus they’re easy enough to whip up on a weekend afternoon when you need something special.

What Kind of Pumpkin Seeds Should I Use?

Raw pumpkin seeds are definitely the way to go for these cookies, and you can use either fresh seeds from a pumpkin you’ve carved or store-bought raw seeds. If you’re using fresh seeds, make sure to clean them thoroughly and remove any pulp – a good rinse and pat dry will do the trick. Store-bought raw pumpkin seeds work just as well and save you some prep time. You’ll want to avoid using roasted or salted pumpkin seeds since the cookies will do their own toasting during baking, and the added salt could throw off the flavor balance.

Options for Substitutions

This cookie recipe is pretty forgiving when it comes to swaps, so here are some options if you need to make changes:

• Raw pumpkin seeds: If you don’t have pumpkin seeds, try sunflower seeds, chopped walnuts, or pecans instead. You could even use toasted coconut flakes for a different twist. Just keep the amount the same.
• All-purpose flour: You can substitute up to half the flour with whole wheat flour for a nuttier flavor, but don’t go beyond that or your cookies might turn out too dense.
• Unsalted butter: Salted butter works fine – just reduce the added salt to ¼ teaspoon. You can also use coconut oil (solid, not melted) but let the dough chill for 30 minutes before baking.
• Brown sugar: If you’re out of brown sugar, mix 1 cup granulated sugar with 1 tablespoon molasses, or just use all granulated sugar (though your cookies will be a bit less chewy).
• Semi-sweet chocolate chips: Feel free to swap these with dark chocolate chips, white chocolate chips, butterscotch chips, or even dried cranberries for a different flavor profile.

Watch Out for These Mistakes While Baking

The biggest mistake when making these cookies is skipping the step to toast your raw pumpkin seeds first – untoasted seeds will taste bland and chewy, so toast them in a dry skillet for 5-7 minutes until golden and fragrant before mixing them into your dough.

Another common error is not bringing your butter to proper room temperature, which should be soft enough to leave a fingerprint when pressed but not melted or greasy, as this affects how well your sugars cream together.

Don’t overbake these cookies since the pumpkin seeds can become tough – they’re done when the edges are set but the centers still look slightly underbaked, and they’ll continue cooking on the hot pan after you remove them from the oven.

For even better results, chill your dough for at least 30 minutes before baking, which prevents the cookies from spreading too much and helps them hold their shape.

What to Serve With Chocolate Chip Pumpkin Seed Cookies?

These cookies are perfect with a tall glass of cold milk for dunking, or try them alongside a warm cup of coffee or hot chocolate for an afternoon treat. I love serving them with vanilla ice cream for a simple dessert, especially when the cookies are still slightly warm from the oven. They also make a great addition to a fall dessert spread alongside apple cider or pumpkin spice lattes. For something a little different, try crumbling them over plain Greek yogurt with a drizzle of honey for a fun breakfast or snack.

Storage Instructions

Keep Fresh: These cookies stay soft and chewy when stored in an airtight container at room temperature for up to a week. I like to toss a slice of bread in the container to help keep them from getting too crispy. Just make sure they’re completely cooled before storing or they’ll get soggy from the steam.

Freeze: You can freeze the baked cookies in a freezer-safe container for up to 3 months, or freeze the cookie dough balls on a baking sheet before transferring to freezer bags. The dough balls can go straight from freezer to oven – just add an extra minute or two to the baking time.

Enjoy: Frozen cookies thaw quickly at room temperature in about 30 minutes, or you can warm them in the microwave for 10-15 seconds to get that fresh-baked taste back. If you froze the dough, bake them straight from frozen and you’ll have warm cookies ready in no time!

Preparation Time	20-30 minutes
Cooking Time	18-20 minutes
Total Time	38-50 minutes
Level of Difficulty	Medium

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 3900-4100
• Protein: 45-55 g
• Fat: 190-210 g
• Carbohydrates: 510-540 g

Ingredients

For the toasted seeds:

• 1 cup raw pumpkin seeds (pepitas)

For the cookie dough:

• 1 tsp salt
• 1 tsp vanilla extract (pure vanilla for best flavor)
• 2 sticks unsalted butter (for better control over sodium)
• 2 large eggs (at room temperature, about 70°F)
• 1/2 tsp baking soda
• 1 cup light brown sugar, packed
• 1 cup white sugar
• 1 cup semi-sweet chocolate chips (I like Ghirardelli)
• 1/2 tsp ground cinnamon
• 2 1/2 cups all-purpose flour (King Arthur is my favorite for cookies)

Step 1: Prepare the Oven and Baking Sheets

Preheat your oven to 350°F (175°C).

Line two baking sheets with parchment paper or a Silpat, and set them aside.

This will prevent the cookies from sticking and make cleanup much easier.

Step 2: Toast the Pumpkin Seeds

• 1 cup raw pumpkin seeds

Spread the raw pumpkin seeds evenly on a large rimmed baking sheet.

Place the sheet on the upper rack of the oven and toast, tossing occasionally, until the seeds are golden brown, about 10 minutes.

Remove the toasted pumpkin seeds from the oven and allow them to cool.

Toasting brings out the nutty flavor, so I never skip this step.

Step 3: Combine the Dry Ingredients

• 2 1/2 cups all-purpose flour
• 1 tsp salt
• 1/2 tsp baking soda
• 1/2 tsp ground cinnamon

In a large bowl, whisk together the all-purpose flour, salt, baking soda, and ground cinnamon.

Mixing the dry ingredients first ensures even distribution of leavening and spice throughout the cookies.

Step 4: Cream Butter and Sugars, Then Add Eggs and Vanilla

• 2 sticks unsalted butter, at room temp
• 1 cup light brown sugar, packed
• 1 cup white sugar
• 2 large eggs
• 1 tsp vanilla extract

In the bowl of a stand mixer, beat the unsalted butter, light brown sugar, and white sugar on medium speed until the mixture is light and fluffy.

Next, add the eggs one at a time, beating well after each addition.

Scrape down the sides of the bowl as needed.

Then add the vanilla extract and beat just until combined.

Step 5: Combine Wet and Dry Ingredients

• dry ingredients from Step 3
• butter and sugar mixture from Step 4

With the mixer on low speed, gradually add the dry ingredients (from Step 3) to the wet mixture (from Step 4) in batches.

Mix until just blended, being careful not to overmix the dough.

Overmixing can make cookies tough, so I always stop as soon as the flour disappears.

Step 6: Fold in Chocolate Chips and Toasted Pumpkin Seeds

• 1 cup semi-sweet chocolate chips
• toasted pumpkin seeds from Step 2

Remove the bowl from the mixer and, using a spatula, gently fold in the semi-sweet chocolate chips and the toasted pumpkin seeds (from Step 2) by hand.

Stir just enough to distribute them evenly throughout the dough.

Step 7: Portion and Bake the Cookies

• cookie dough from Step 6

Using a large cookie scoop, portion the dough onto the prepared baking sheets, leaving at least 2 inches between each mound to allow for spreading.

Bake in the preheated oven for about 18 minutes, or until the edges are lightly browned but the centers remain soft.

For a gooier center, I sometimes pull the cookies out just before the centers are fully set.

Step 8: Cool the Cookies

Transfer the baked cookies onto wire racks and allow them to cool completely.

This helps set their texture and makes them easier to store.