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Hello! I’m Anjali. I’m a board certified health coach, author, wife, mom and food lover from the SF Bay area (now living in Seattle, WA!); with a passion for delicious food and a desire to make healthy eating easy, tasty and fun! Learn more about me here and stay for a while!

Anjali Shah

Healthy Pumpkin Brownies

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These easy healthy pumpkin brownies are not only fudgy, chocolatey, and decadent, but they’re actually healthy too! Only 15 minutes of prep time, less than 150 calories per serving, and the perfect fall dessert!

Healthy pumpkin brownies stacked on a white pedestal, with cinnamon, chocolate chips and pumpkin in the background.

Pumpkin season is my favorite time of year, and I absolutely love brownies! They’re one of the best desserts. This is why, when fall comes around, easy pumpkin brownies are a fun way to switch things up! This layered healthy pumpkin brownie recipe is thick, chewy, and sweet — it will fill your house with the most amazing fall scents.

Typically when I bake, I try to keep all of the decadent flavors of traditional fudgy brownies, while still making a few healthy swaps to lighten things up just a bit! There is still sugar in this recipe, just a little less of it. There is still butter, but some of it has been replaced with a healthier alternative.

The best part is you can enjoy these healthy chocolate pumpkin brownies relatively guilt-free, while still making an amazing dessert from scratch! This recipe is sure to become one of your favorite fall treats to satisfy your sweet tooth!

👩🏽‍🍳 Why You’ll Love These Healthy Pumpkin Brownies

  • Quick And Easy Without A Box Mix: You can make these simple brownies made with canned pumpkin in nearly the same amount of time it would take to prep a box mix.
  • Gluten-Free Option: You can easily make these scrumptious pumpkin puree brownies without any gluten.
  • Vegan Option: With just a few swaps, you can make these low fat pumpkin brownies vegan-friendly!
  • Best Healthy Pumpkin Brownies Ever: I haven’t found a better version of these brownies yet! 
  • Simple Ingredients: All of the ingredients are easy to find at the grocery store – or might be in your kitchen already!
  • Way Better For You Than Traditional Brownies: There are a number of substitutes in this easy brownie recipe that makes it a better option for healthy snacking.

Latest Recipe Video!

🥘 Ingredients

All you need are some super-simple ingredients to make this healthy pumpkin brownies recipe.

This recipe is packed with healthy ingredients to make these pumpkin chocolate chip brownies better for you than their traditional counterparts! For the full ingredients list and instructions, see the recipe card below.

Ingredients for easy layered healthy pumpkin brownies recipe on a white background.
  • Whole Wheat Pastry Flour: Higher in fiber and less processed than regular all-purpose flour. 
  • Brown Sugar: Instead of the usual amount of sugar, I’ve reduced the amount of total sugar to 1/3 cup. For an unrefined sweetener option, you could also use maple syrup for this healthy brownie recipe.
  • Unsweetened Applesauce and Butter: An easy healthy swap for butter is unsweetened applesauce. When used in combination with butter, you still get a decadent and fudgy brownie, but with fewer calories. 
  • Flax Egg: Low calorie, high fiber, and rich in Omega-3s, replaces eggs in this recipe for chocolate pumpkin brownies.
  • Cacao Powder and Dark Chocolate Chips: Cacao powder is rich in antioxidants and brings a deep dark chocolate flavor to these healthy brownies made with pumpkin puree. I like to use 70% dark chocolate or higher. 
  • Canned Pumpkin Puree: Be sure to use pure pumpkin puree and not pumpkin pie filling. 
  • Spices: You need a little bit of cinnamon, ground cloves, nutmeg, and vanilla extract for this healthy pumpkin dessert recipe.

🍲 Ingredient Substitutions

  • Butter Alternatives: Coconut oil, pureed avocado, almond butter, or whole milk Greek yogurt are all great alternatives for butter.
  • Chocolate Substitute: You can use baking chocolate instead of cacao powder for this pumpkin chocolate brownie recipe.
  • Homemade Puree: You can also make your own pumpkin puree (instead of using canned) by taking the whole pumpkin, steaming it, and pureeing it in a blender.

🔪 How To Make Healthy Pumpkin Brownies

Here’s how to make this easy pumpkin brownie recipe. For more detailed instructions and nutrition facts, see the recipe card below.

Mix Dry Ingredients: Preheat oven to 350°F. Line an 8×8 baking dish with parchment paper or spray with cooking spray. In a large bowl, combine the flour, salt and baking powder. Set aside.

Mix Wet Ingredients: In another bowl, cream together the sugar and butter. Then mix in the flax eggs, applesauce, and vanilla until well combined.

butter and sugar creamed in a bowl

Combine Wet And Dry Ingredients: Pour wet ingredients into dry ingredients. Stir together with a spatula just until well combined. Then pour half of this batter into the other bowl.

wet and dry ingredients mixed together in a bowl

Prepare Chocolate Batter: To the first bowl, fold in the soy milk, cocoa powder, and chocolate chips.

chocolate chips added to batter

Make Pumpkin Batter: To the second mixing bowl, stir in pumpkin puree and the spices. So you’ll have two bowls of batter – one with pumpkin, one with the chocolate mixture.

pumpkin batter in a bowl

Prepare Chocolate Base: Pour the chocolate brownie batter into the baking dish and spread in an even layer across the bottom.

chocolate batter spread in a pan

Add Pumpkin Batter: Then pour the pumpkin batter on top and spread in an even layer.

pumpkin batter spread on top of chocolate batter

Bake: Place in your preheated oven and bake for 25-30 minutes, or until a toothpick inserted comes out clean. Allow these healthy pumpkin chocolate brownies to cool to room temperature before cutting and serving.

Low calorie, healthy pumpkin brownies on parchment paper.

💭 Expert Tips

  • Tap The Pan On The Counter: After adding the batter, lift the pan and tap it on the counter several times to eliminate air bubbles and even out the batter. 
  • Mix Separately: Always mix wet ingredients separately and dry ingredients separately before combining them so that the dry ingredients are evenly dispersed. 
  • Add Wet To Dry: Add the wet ingredients to the dry ingredients rather than vice versa. It will make it much easier to mix.
  • Extra Parchment Paper: If you can, use parchment paper rather than cooking spray. This way, you can use a bit extra to drape over the sides of the baking pan, which makes it easy to life the whole pan of brownies out of the pan once cooled.
  • The Best Cocoa Powder For Baking: Typically, I recommend buying a natural, organic, Dutch process cocoa powder, because it has a higher fat content and a deep chocolate flavor. It works great in this layered pumpkin brownies recipe.
  • Use A Paper Towel: For clean slices, wipe the knife clean with a damp paper towel after each slice.

📖 Variations

You can change up these sweet treats in a bunch of different ways! 

  • Make Pumpkin Muffins: You can easily turn this recipe into healthy pumpkin brownie bites by using a muffin tin instead of a baking dish. To make muffins – preheat the oven to 375, spray your muffin tin with cooking spray or line with cupcake liners, fill each cup about 3/4 full, and bake for 25-30 minutes or until a knife inserted in the center of a muffin comes out clean.
  • Healthy Banana Pumpkin Brownies: Use pureed banana instead of the applesauce in this recipe!
  • Flourless Pumpkin Brownies: Use this recipe for flourless gluten free brownies for your brownie batter, and make the pumpkin layer as directed in this recipe – then combine the two!
  • Healthy Pumpkin Protein Brownies: Add one scoop of your favorite chocolate protein powder to the batter!

🍽 Serving Suggestions

  • Ice Cream: Add a big scoop of your favorite ice cream over top of these pumpkin fudge brownies. Try it with this chocolate tofu ice cream, lychee ice cream, or caramel nice cream!
  • Coffee: Chocolate is a perfect pairing for a warm cup of coffee — or an iced version. Sprinkle a little pumpkin spice in it to really complement the brownie. For a twist on regular coffee, try these cocoa pumpkin brownies with this beetroot latte or mocha latte!
  • Milk: Pour a cold glass of milk or your favorite milk alternative. You could also serve it with chocolate milk tea!
  • Fruit: Fresh fruit can brighten up the presentation and create the perfect flavor contrast. I love these pumpkin spice brownies with berries on the side!
  • Toppings: Treat these chewy pumpkin brownies to a caramel sauce, fresh whipped cream, a sprinkle of sea salt, or a chocolate drizzle over the top.

🙌 Dietary Adaptations

  • Gluten-Free Option: For gluten-free pumpkin brownies, use Bob’s Red Mill 1:1 Gluten-Free Baking Flour. Another option for gluten-free flour includes almond flour, oat flour, coconut flour, or buckwheat flour.
  • Healthy Vegan Pumpkin Brownies: Use 1/2 cup coconut oil or 1/2 cup pureed avocado instead of butter, and make sure your chocolate chips are dairy free.
  • Sugar-Free Option: Use powdered monk fruit or your favorite alternative sweetener. Coconut sugar is another good alternative if you’re just looking for a refined sugar free recipe (vs. zero sugar brownies).

🫙 Storage Directions

  • Store At Room Temperature: Store these easy homemade brownies in an airtight container at room temperature and enjoy them the next day. They will actually last for up to 4 days (but I’d be surprised if they were around that long! 🙂 ).
  • To Refrigerate: If you have any extra brownies left after 4 days, you can get a couple more days of shelf life out of them by putting them in the fridge. To reheat, just microwave them for 20 seconds.
  • To Freeze: Wrap leftover pumpkin brownies tightly in plastic wrap and freeze for up to 3 months.

❓Recipe FAQs

Can I use pumpkin instead of oil in brownie mix?

Absolutely! Unsweetened pumpkin puree can be used as a 1:1 replacement for oil when making brownies. So 1 cup of oil = 1 cup pumpkin puree. If the recipe calls for butter, you can substitute ¾ cup pumpkin puree for 1 cup of butter.

How do you substitute pumpkin puree for baking?

If you can’t find pumpkin puree, you can still make these low calorie pumpkin brownies by using sweet potato puree or butternut squash puree! It will have a very similar flavor when done!

What makes brownies more chewy?

There are a couple ways to make chewy brownies vs. cakey or fudgy pumpkin brownies. The first is to use a combination of vegetable oil and butter, the second is to slightly underbake your brownies by 1-2 minutes, and the third is to put them in the fridge after they’ve been baked for up to 1 hour. Then you will get a chewy dense brownie that will satisfy your sweet tooth!

Can you substitute cocoa powder for chocolate in brownies?

You can, but keep in mind that your brownies will be less sweet if you use cocoa powder as a substitute for chocolate! To substitute cocoa powder: Combine 3 tablespoons of unsweetened cocoa powder + 1 tablespoon of coconut oil. That is the equivalent of 1 ounce of chocolate.

Easy healthy pumpkin brownies on parchment paper.

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5 from 33 votes

Healthy Pumpkin Brownies

These layered, low calorie, healthy pumpkin brownies are not only fudgy, chocolately and decadent, but they're actually healthy too! Only 15 minutes of prep time, less than 150 calories per serving, and the perfect fall dessert!
Prep Time15 minutes
Cook Time45 minutes
Total Time1 hour
Course: Baking, Dessert
Cuisine: American
Diet: Low Calorie, Vegetarian
Servings: 12 pieces
Calories: 140kcal
Author: Anjali Shah



  • Preheat oven to 350°F. Line a 8×8 baking dish with parchment paper or spray with cooking spray. In a large bowl, combine the flour, salt and baking powder. Set aside.
  • In another bowl, cream together the sugar and butter. Then mix in the flax eggs, applesauce and vanilla until well combined.
  • Pour wet ingredients into dry ingredients. Stir together with a spatula just until well combined. Then pour half of this batter into the other bowl. To the first bowl, fold in the soy milk, cocoa powder and chocolate chips.
  • To the second bowl, stir in pumpkin puree and the spices.
  • Pour the chocolate batter into the baking dish and spread in an even layer across the bottom.
  • Then pour the pumpkin batter on top and spread in an even layer.
  • Bake in preheated oven for 25-30 minutes, or until a toothpick inserted comes out clean. Allow to cool to room temperature before cutting and serving.


  • Make sure you use unsweetened pumpkin puree, not pumpkin pie filling for this recipe (they are basically on the same shelf at the grocery store, so be sure to grab the right one!)
  • To mix things up, you can add chopped walnuts or pecans to this recipe! You can add 1/4-1/2 cup chopped nuts to the chocolate part of the batter before spreading in the baking dish.
  • For a gluten free option, use Bob’s Red Mill 1:1 Gluten Free Baking Flour as a 1:1 replacement for the flour in this recipe.
  • If you don’t have cinnamon, cloves and nutmeg, you can use the equivalent amount of pumpkin pie spice (3 tsp total) in this recipe.
  • Make sure to use unsweetened cacao powder (not unsweetened cocoa powder) in this recipe. Cacao is less processed and has a milder taste so it works better for these brownies!
  • Let the brownies rest before cutting into squares – you’ll end up with a much better, held-together brownie that way.
  • You can decrease the amount of brown sugar even more in this recipe for an even healthier version — it’ll still be slightly sweet from the pumpkin and chocolate chips!
  • Note: These brownies are not overly sweet. They have more of a dark chocolate flavor. If you want a sweeter, more traditional brownie, you will have to increase the sugar (up to 1 cup for a traditional brownie level of sweetness). But that will give each brownie about 27 grams of sugar, making it much more like a traditional brownie, but not as healthy for you!
Note: Nutrition info calculated using whole wheat pastry flour, 1/3 cup brown sugar, applesauce + butter and flax eggs


Serving: 1brownie | Calories: 140kcal | Carbohydrates: 21.2g | Protein: 2.1g | Fat: 7g | Saturated Fat: 4.1g | Sodium: 177.1mg | Potassium: 25mg | Fiber: 2.9g | Sugar: 9.8g

64 responses to “Healthy Pumpkin Brownies”

  1. I love the layers! These turned out so good, I’ll make them often this fall and tuck them into the kids’ lunch boxes for a healthy snack.5 stars

  2. These healthy pumpkin brownies are perfect for my kids lunches this october! Saving this recipe for pumpkin season!5 stars

  3. I love this layered look. These brownies are so perfect for the fall! Making them this weekend, thank you so much for the recipe 🙂5 stars

  4. I love that these are that bit healthier and they look great with the two layers, too. Looking forward to giving these a try.5 stars

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