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The Best Ever Healthy Pumpkin Chocolate Chip Cookie Recipe

This healthy pumpkin chocolate chip cookie recipe has been my go-to for over 15 years. They’re made with whole wheat flour and coconut sugar and aren’t overly sweet. 

Well friends, it’s officially fall! This weather has been so crispy and perfect, 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? Last week was pumpkin bread and this week is pumpkin cookies.

This Chocolate Chip Pumpkin Cookie recipe is a REALLY good one, and even better since it’s a much healthier option than most recipes. It uses coconut sugar and whole wheat flour and the cookies come out light and fluffy, with an almost spongecake-like texture. Certainly, these will melt in your mouth!

melt in your mouth chocolate chip cookie

I kid you not, when I made these, I ate about three cookies worth of batter and then I ate about 10 cookies, five while cooling (they’re so good warm!) and another five after I took photos (also so delicious once cooled). Can you spot the half eaten cookies on the cooling rack? Oops. I should have removed my evidence before I snapped photos. But if you want proof that using less processed options when baking makes a big difference in how it makes you feel, I didn’t feel awful after 10 cookies. A little full yes, but not like death, which is certainly the case when I eat more than 1-2 cookies made with white sugar and white flour.

pumpkin chocolate chip cookies

But, 10 cookies in, I decided I needed to get some out of the house so I took a plate over to our new neighbor. She’s getting married this weekend and they have a bunch of kids. I don’t know exactly how many, anything over 1 is “a bunch” to me. (Never mind I grew up with five older brothers, who now all have four kids each). Anyway, it felt like a neighborly thing to do, taking freshly baked cookies to the neighbor family, since I’d been meaning to take something over anyway. But in reality, it was a bit selfishly driven since I had to get some of these out of the house before I ate the entire batch.

Thankfully this pumpkin chocolate chip cookie recipe makes a LOT of cookies, so there were still plenty to keep at home. My husband, Tommy, was happy to come home from a rough day at work to freshly baked cookies. And I was happy to tell him that I also had a rough day of work, making cookies. While I loved my corporate career and sometimes mix that world, I do love that one of my jobs now is to make cookies, photograph it and eat it. (Hey, I gotta test the end result for y’all!)

I fully intend to eat more cookies with coffee in the morning. Hey, they’re healthy-ish so yes, I’m going to eat one (or a bunch, if you will) with breakfast. Okay, let’s get onto the recipe and some recipe notes!



chocolate chip cookie dough

Pumpkin Puree vs. Pumpkin Pie Filling

Firstly, 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. 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 not a good thing. So check your labels people!

A few additional notes about this ingredients, substitutions, and kitchen tools before you get started.

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!


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. 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!


I use coconut sugar in almost all my baking but you can sub 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 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.

Chocolate chips:

I like the extra dark Guittard chocolate chips, but whatever your favorite chocolate chips are will work just fine!

Cream Cheese Frosting:

Since these have chocolate chips, I don’t feel like they need frosting. But I know a LOT of pumpkin cookies you find in bakeries are topped with a cream cheese frosting. This is my go-to cream cheese frosting recipe if you go that route! (The frosting recipe is at the bottom! Cut it in half since that makes enough for a cake.)

Kitchen and Baking tools

You could mix this by hand, but I recommend a hand mixer. For instance, I use this hand mixer which is a great price point for a mixer I’ve had 10+ years.

Meanwhile, I like a small cookie so I used a small cookie dough scoop, but 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.

I prefer to line baking sheets with parchment paper vs. spraying the pan with non-stick spray since it makes clean up easier.

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


pumpkin chocolate chip cookies

Do you have any fall traditions that are starting back up in your home? I love to bake, of course, lots of pumpkin flavored recipes, and Tommy and I love to go to the mountains in the fall. Moreover, I also love a long run when the weather is super crisp. There’s something about the fall that just makes life so much more fun and cozy!

melt in your mouth chocolate chip cookie

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


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



  • 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


  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, applesauce, 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.


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?


  • 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 something you bake that officially signals fall to you? Pumpkin cookies and pumpkin bread are my must-bakes before it’s really fall for me.

Get the tools to make cookies

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  • Reply

    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]

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

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