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The Best Ever Healthy Pumpkin Chocolate Chip Cookie Recipe

It’s officially fall! So, I thought I’d reshare this yummy and healthy pumpkin chocolate chip cookie recipe that has been my go-to for over 15 years. Seriously, these cookies make me want to curl up in a cozy blanket in front of a roaring fireplace. Never mind we can’t actually use our fireplace (long story). But, I will be doing a lot of curling up in the next few weeks once our baby arrives! So I obviously need some cookies for that.

The weather has been teasing us with some perfectly, crisp days which means it’s a perfect time for baking. Once the temperatures drop, I want to spend more time in the kitchen and particularly more time baking. And what’s fall without making a few pumpkin recipes?

This Chocolate Chip Pumpkin Cookie recipe is a REALLY good one, and a much healthier option than most recipes. This recipe also uses coconut sugar and whole wheat flour and the cookies come out light and fluffy, with an almost sponge cake-like texture. And the cooled cookies are just as good as the warmed ones! Okay, so let’s dive into some recipe details!

healthy pumpkin chocolate chip cookie healthy pumpkin chocolate chip cookie

The Best Ever Healthy Pumpkin Chocolate Chip Cookie Recipe

Pumpkin Puree vs. Pumpkin Pie Filling

First, let’s talk about canned pumpkin. Some people get confused between pumpkin puree and pumpkin pie filling. The difference is that a pumpkin puree is nothing but pumpkin. In fact, pumpkin pie filling is pre-mixed mixed with spices and sweeteners.

If you’re going to make a pumpkin recipe from scratch, you want pumpkin puree. It allows you to add your own sweetener and spices and gives you more control when it comes to crafting your own recipe.

For this recipe, make sure you use plain pumpkin puree, like this canned pumpkin, not canned pumpkin pie filling. If you add spices and sugar to an already spiced pumpkin mix, it’ll be overly spiced, and yes, that it is a thing. And it’s also not a good thing. So check your labels people!

Ingredients

This pumpkin chocolate chip cookie recipe makes a LOT of cookies, so you will have plenty of leftovers. They freeze well though, so fret not! And they make neighbors happy so you could leave some on porches and become even more popular in your neighborhood.

1 cup canned pumpkin (NOT pumpkin pie mix)
3/4 cup coconut sugar
1/2 cup unsweetened applesauce
1 egg
1 tablespoon vanilla extract
2 cups whole wheat flour
2 teaspoons baking powder
2 teaspoons cinnamon
1/8 teaspoon nutmeg
1/8 teaspoon ground cloves
1/2 teaspoon salt
1 teaspoon baking soda
1 cup semi-sweet or dark chocolate chips

healthy pumpkin chocolate chip cookie healthy pumpkin chocolate chip cookie

Instructions

Step 1

Preheat the oven to 350 degrees.

Step 2

Prepare two baking sheets by lining with parchment paper.

Step 3

In a large bowl, cream together pumpkin, sugar, applesauce, egg and vanilla and mix well. You should have a fluffy, light brown mixture.

Step 4

In a medium bowl, whisk together flour, baking powder, cinnamon, nutmeg, cloves, salt and baking powder in a separate bowl.

Step 5

Gradually add the dry mixture to wet and mix until just combined. Don’t over-mix it!

Step 6

Fold in chocolate chips.

Step 7

Use a small ice cream scoop to form the cookies and place 1-1.5? apart. They don’t spread so they can be close.

Step 8

Bake for 7-9 minutes until they feel springy when you touch them. Don’t over-bake!

Step 9

Remove to a wire rack to cool.

Step 10

Try not to eat ALL of the cookies. Trust me, this step is hard.

Ingredients and substitutions

Pumpkin Pie Spice

I haven’t tried using pumpkin pie spice in place of the individual spices listed. So if you do, leave a comment and let us know how it turns out!

Flours

I used One Degree Sprouted Whole Wheat Flour but any whole wheat flour will work. Also, I’ve never made these with all-purpose flour, but I’m sure it’d be just fine. In fact, I have made them with gluten-free flour and they did NOT turn out well. But every gluten-free flour blend is different, so again, experiment and let us know how it goes! I can’t guarantee they’ll turn out the same if you start subbing a bunch of things, but hey, that’s half the fun of baking!

Sugar

I use coconut sugar in almost all my baking but you can substitute regular granulated sugar in this recipe. Coconut sugar is caramel colored and tastes similar to brown sugar and works beautifully as a substitute for cane sugar in most recipes. I used coconut sugar since I like the deeper flavor it gives recipes. It still has the same calories as granulated sugar, so you’re not saving on calories by subbing white sugar for coconut sugar.

Dr. Weil, one of my favorite health experts, explains that coconut sugar is about 70-80% sucrose and only 3-9% percent each of both fructose and glucose. “This is an advantage because you want to keep your consumption of fructose as low as possible, and cane sugar is 50 percent fructose.” Read more about coconut sugar here.

Egg

If you want to make fully vegan cookies, try substituting the egg for 1 Tablespoon of flaxseed (soaked in 3 Tablespoons of water). Or use ¼ cup of chickpea brine (the liquid from the can) and whip it up before adding into the recipe.

I haven’t actually tried this substitution for these cookies, so if you attempt it, let us know how it goes in the comments!

Chocolate chips

I like the extra dark Guittard chocolate chips or the Enjoy Life Dark Chocolate mini chips, but whatever your favorite chocolate chips are will work just fine!

Cream Cheese Frosting

I’m not a big frosting person but my husband is, so I typically frost about half of these! And if you want to recreate your favorite bakery’s pumpkin chocolate chip cookies, you’ll probably want to pair these with a cream cheese frosting.

So, for your frosting lovers, I shared my go-to cream cheese frosting recipe as well, at the bottom of the post. Cut it in half since this recipe is supposed to make enough for a cake.

Baking Notes

Mixing the recipe

You could mix this by hand, but I recommend a hand mixer. This is the hand mixer I’ve had for 10+ years.

Scooping the cookies

I like having small cookies, so I use a small cookie dough scoop. If you prefer larger cookies, use a large scoop. However, you’ll need to adjust the bake time a little bit since those will take longer to bake.

Note: If you like a slightly flatter cookie, press each mound down with the back of the ice cream scoop.

Baking the cookies

I prefer to bake one sheet at a time to ensure even baking. This means that to bake all the cookie dough, this recipe requires 3 baking sheets (1 for each round).

So the cooking time is 7-9 minutes per round. Times by 3x and you get 21-30 minutes total baking time to make the full recipe (as noted above). Or, just bake the amount of cookies you want to today and refrigerate the rest of the dough (more on that below).

I usually prep two sheets so I can put the second one in as soon as the first comes out. Then, I let the first pan cool a bit before reloading with dough to bake for the third and last round.

I also line baking sheets with parchment paper rather than spraying the pan with non-stick spray since it makes clean up so much easier.

These are the baking sheets I use. I have three different sizes and love them all!

How long will leftovers last?

These cookies are best eaten the same day but still fine in an airtight container for 3-4 days. But they just tend to a get al little sticky once you store them. For that reason, I recommend baking them in small batches and baking just what you need for the day. You can refrigerate the rest of the dough for 3-4 days until you’re ready to bake more.

Can I freeze the leftover cookies?

You can also freeze the baked cookies in an airtight container for 2 months. Let them thaw at room temperature before eating. (I froze a batch to have on hand after the baby comes!!)

Nutrition

Serving Size: 1 cookie
Calories: 57
Sugar: 5.3
Sodium: 77.3
Fat: 1.6
Saturated Fat: 0.8
Trans Fat: 0
Carbohydrates: 9.8
Fiber: 1.6
Protein: 1.2
Cholesterol: 4.1

Do you have any fall traditions that are starting back up in your home?

 

 

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The Best Ever Healthy Pumpkin Chocolate Chip Cookie Recipe

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  • Author: Teri
  • Prep Time: 15 minutes
  • Cook Time: 30 minutes
  • Total Time: 45 minutes
  • Yield: 45 small cookies 1x
  • Category: Dessert
  • Method: Baking

Description

The yummiest, healthy pumpkin chocolate chip cookies. The cookies are light and fluffy with the perfect pumpkin flavor without being overly sweet.


Scale

Ingredients

  • 1 cup canned pumpkin (not pumpkin pie mix)
  • 3/4 cup coconut sugar
  • 1/2 cup softened butter
  • 1 egg
  • 1 tablespoon vanilla extract
  • 2 cups whole wheat flour
  • 2 teaspoons baking powder
  • 2 teaspoons cinnamon
  • 1/8 teaspoon nutmeg
  • 1/8 teaspoon ground cloves
  • 1/2 teaspoon salt
  • 1 teaspoon baking soda
  • 1 cup semi-sweet or dark chocolate chips

 

Cream cheese frosting ingredients (optional)

  • 1/2 cup butter, softened
  • 8 ounces cream cheese
  • 4 cups confectioners’ sugar
  • 2 teaspoons vanilla extract
  • 1 teaspoon lemon zest (optional)

Instructions

  1. Preheat oven to 350 degrees.
  2. Prepare two baking sheets by lining with parchment paper.
  3. In a large bowl, cream together pumpkin, sugar, butter, egg and vanilla and mix well. You should have a fluffy, light brown mixture.
  4. In a medium bowl, whisk together flour, baking powder, cinnamon, nutmeg, cloves, salt and baking powder in a separate bowl.
  5. Gradually add the dry mixture to wet and mix until just combined. Don’t over-mix it!
  6. Fold in chocolate chips.
  7. Use a small ice cream scoop to form the cookies and place 1-1.5″ apart. They don’t spread so they can be close.
  8. Bake for 7-10 minutes until they feel springy when you touch them. Don’t over-bake!
  9. Remove to a wire rack to cool.

Cream Cheese Frosting:

  1. Beat the butter and cream cheese until well combined.
  2. Gradually add the sugar and beat, and then add the vanilla extract and lemon zest (if using) until fully combined.
  3. Frost cookies once they are completely cooled.
  4. Store leftover frosting in the fridge for a week or freezer for 2 months.

Notes

If you like a slightly flatter cookie, press each mound down with the back of the ice cream scoop.

This required three sheet pans to bake all the dough, so the cook time is 7-10 minutes per round. (The recipe notes at the top lists the total time baking so you have an accurate estimate of how long it’ll take to make the full recipe.)

I prefer to bake one sheet at a time to ensure even baking. But, I prep two sheets so I can put the second one in as soon as the first comes out. Then, I let the first pan cool a bit before reloading with dough to bake for the last round.

These are best eaten the same day but still fine in an airtight container for 3-4 days. However, I do recommend baking them in small batches and baking just what you need for the day. (You can refrigerate the rest of the dough for 3-4 days until you’re ready to bake more.) Who doesn’t love daily, freshly-baked cookies?


Nutrition

  • Serving Size: 1 cookie
  • Calories: 57
  • Sugar: 5.3
  • Sodium: 77.3
  • Fat: 1.6
  • Saturated Fat: 0.8
  • Trans Fat: 0
  • Carbohydrates: 9.8
  • Fiber: 1.6
  • Protein: 1.2
  • Cholesterol: 4.1

Get the tools to make cookies

This recipe was originally shared on my blog in 2010 and again in 2018. I updated it this year to address some of the stickiness that people experienced, using butter instead of applesauce. I hope you love this updated version and enjoy the photos that got a major upgrade! Here are some of the old photos. 🙂

pumpkin cookies

melt in your mouth chocolate chip cookie healthy pumpkin chocolate chip cookie

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4 Comments

  • Reply
    CAroline
    at

    How would these be with no choc chips. Thinking of making them for a preschool class but they don’t allow chocolate. Just curious if you rec a sub or just leaving them out. THEy are nut free and dairy free so I’m subbing almond milk already. :P. Thanks

    • Reply
      Teri [a foodie stays fit]
      at

      They’re still great! You could sub in dried fruit (raisins? cranberries? cherries?) if you still want a little texture!

  • Reply
    Natalie
    at

    These look delicious! I’m a fan of anything that involves pumpkin and chocolate 🙂 I do happen to be one of those people who love frosting, but didn’t see the recipe at the end of the post? Thank you so much for sharing! 🙂

    • Reply
      Teri [a foodie stays fit]
      at

      oops! Thanks for letting me know I forgot to add that in! It’s just a simple recipe!

      ½ cup butter, softened
      8 ounces cream cheese
      4 cups confectioners’ sugar
      2 teaspoons vanilla extract

      Beat the butter and cream cheese until well combined. Gradually add the sugar and beat, and then add the vanilla extract until fully combined. Enjoy!

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