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Healthy Chocolate Pumpkin Muffins are a must-have for fall! And, you don't have to resist either. They're made with whole wheat flour, Greek yogurt, cocoa powder, and lots of pumpkin and are absolutely irresistible!
We "chocolatized" Greek yogurt pumpkin muffins, one of our most popular Fall Recipes. Because chocolate makes everything better! Are you with me? 🙂
In this case, chocolate does NOT mean unhealthy. We used our master muffin mix with Greek yogurt, whole wheat pastry flour, and less refined sugar. They're naturally packed with extra protein so they're anytime muffins...as in you can have them for a snack, dessert, or even breakfast!
Ingredients in Healthy Chocolate Pumpkin Muffins
As we always say, healthy means something different to everyone. With that in mind, here are the key ingredient swaps we made from a traditional muffin recipe and a few other substitutions we've tried.
- Whole wheat pastry flour is our go-to flour for all of our Bread and Muffin Recipes.
- Why do we like this type of flour?
- The entire wheat berry is ground (germ, bran and all) just like whole wheat flour. But, a "soft" wheat berry is used instead of the "hard" one used in whole wheat flour. Whole wheat pastry flour is finely ground so it's lower in protein and gluten. It has a mild flavor and works well with baked goods.
- Other Options:
- White whole wheat flour
- 100% whole wheat flour
- A mixture of whole wheat and all-purpose flour (try ½ and ½)
- Unbleached all-purpose flour
- Why do we like this type of flour?
- Greek Yogurt replaces the oil that is often used in muffin recipes. It typically comes in a 5.3 ounce container. Scrape it all in. No measuring required.
- Oil can be used instead. Watch the batter consistency and possibly use less milk.
- Unsweetened Cocoa Powder. Even better, try unsweetened dark chocolate cocoa powder!
- Milk gets the batter for these chocolate pumpkin muffins to the right consistency. Most any milk will work, including almond milk. We used skim in the muffins pictured.
- Dark Chocolate Chips adds more chocolate flavor. You know how it goes, the darker the better. Of course, any chip will work. If you can find them, use mini chocolate chips to more easily distribute through all the muffins.
- Sugar! We used a ½ cup of sugar. That's not much distributed across 16 muffins in my book. It works out to be 1.5 teaspoons per muffin. We've used stevia/sugar blends before and they will work. So, if that's what you normally use for baking, go ahead and substitute it according to the directions for the replacement.
- Egg - One egg or egg-replacer will work in this recipe.
- Pumpkin puree from a can (that's what we used) or check out How to Make Pumpkin Puree by Jessica Gavin.
- Salt, baking powder, baking soda, cinnamon, and vanilla round out the ingredient list.
If you're looking for a gluten-free version, then check out Healthy Oatmeal Pumpkin Muffins which could easily receive the same makeover!
Directions with Pictures
Once the recipe ingredients are gathered, these healthy chocolate pumpkin muffins are a breeze to make!
First mix the dry ingredients together: flour, sugar, cocoa powder, salt, baking powder, baking soda, and cinnamon.
Next, add the wet ingredients: pumpkin puree, Greek yogurt, vanilla extract, egg, and milk. Stir until well-combined. The batter should be thick enough to stick to a spoon for a few seconds.
Fold in chocolate chips. We used 60% cacao dark chocolate chips.
Use paper inserts or don't. Either way, spray the muffin pan with non-stick cooking spray. Fill the wells about ⅔ full of batter. An ice cream scoop with a lever makes quick work of this task.
Bake healthy chocolate pumpkin muffins in a 350 degree Fahrenheit oven for about 25 minutes or until the top is firm.
Allow them to cool in the pan for 5-10 minutes and then ENJOY!
Expert Tips for the BEST Chocolate Pumpkin Muffins
- IF you use a different flour, then you MAY need to adjust the milk accordingly. Start with a small increment, like 1 teaspoon.
- Add a little extra milk if using 100% whole wheat flour.
- Start with a quarter cup of milk if using regular pastry flour and add the remaining milk back as needed.
- The batter should be thick and stick to a spoon for a few seconds. (See the picture above.)
- Spray the cupcake tin with non-stick cooking spray. If you're using paper inserts spray the inside of those too! Otherwise, the muffins will stick to the pan because there is no oil!
- Did you forget to spray the well? Eventually, the moisture will settle and it will be easier to remove the paper liner...if you can wait!
- Sift the cocoa powder to remove the tiny clumps before you measure it out!
- Gently spoon the flour into the measuring cups. I don't sift the flour (although it's not a bad idea.) You don't want to "pack" it or the batter will be too thick.
- Use an ice cream scoop with a quick release to easily and consistently dish out the batter. We used a blue thumb presser that measures a quarter cup.
- Allow muffins to cool in the tin for 5-10 minutes.
- Make an extra batch of the dry ingredients and store in a tightly sealed jar so the muffins are even easier to make the next time.
- Store chocolate pumpkin muffins in an airtight container for 2-3 days. Or, store in the freezer for about 2 months.
They are sure to be a winner with friends and family!
Would you like more easy, healthy, carb-conscious recipes?
📋 Recipe
Healthy Chocolate Pumpkin Muffins
Ingredients
- 1½ cup whole wheat pastry flour
- ¼ cup unsweetened cocoa powder
- ½ cup sugar
- ½ teaspoon baking powder
- ½ teaspoon baking soda
- ½ teaspoon salt
- ½ teaspoon ground cinnamon
- 15 ounce pumpkin puree
- 1 teaspoon vanilla extract
- ⅓ cup skim milk
- 1 egg beaten
- 5.3 ounce non-fat Greek yogurt
- ½ cup chocolate chips preferably dark
Instructions
- Preheat oven to 350 degrees F.
- Combine flour, cocoa powder, sugar, baking powder, baking soda, salt and cinnamon in a bowl.
- Stir pumpkin, vanilla extract, milk, egg and Greek yogurt into the dry mix.
- Fold in mini chocolate chips.
- Fill muffins tins lined with paper liners or coated with cooking spray about ⅔ full. (Tip: if using liners, give them a light spritz of cooking spray before filling them with batter.)
- Bake for 20-25 minutes or until firm.
- Allow muffins to cool for 5 minutes and then remove to a wire rack to cool further.
Notes
- IF you use a different flour, then you MAY need to adjust the milk accordingly. Start with a small increment, like 1 teaspoon.
- Add a little extra milk if using 100% whole wheat flour.
- Start with a quarter cup of milk if using regular pastry flour and add the remaining milk back as needed.
- The batter should be thick and stick to a spoon for a few seconds. (See the picture above.)
- Spray the cupcake tin with non-stick cooking spray. If you're using paper inserts spray the inside of those too! Otherwise, the muffins will stick to the pan because there is no oil!
- Did you forget to spray the well? Eventually, the moisture will settle and it will be easier to remove the paper liner...if you can wait!
- Sift the cocoa powder to remove the tiny clumps before you measure it out!
- Gently spoon the flour into the measuring cups. I don't sift the flour (although it's not a bad idea.) You don't want to "pack" it or the batter will be too thick.
- Use an ice cream scoop with a quick release to easily and consistently dish out the batter. We used a blue thumb presser that measures a quarter cup.
- Allow muffins to cool in the tin for 5-10 minutes.
- Make an extra batch of the dry ingredients and store in a tightly sealed jar so the muffins are even easier to make the next time.
- Store chocolate pumpkin muffins in an airtight container for 2-3 days. Or, store in the freezer for about 2 months.
Michelle says
So, what makes them more healthy than other muffins? The fact that you added greek yogurt?🤭
Marjory Pilley says
There are a few things that make this a healthier muffin in my opinion. It does use Greek yogurt instead of oil. But, it also uses whole wheat flour instead of white and uses a reduced amount of sugar, which can be reduced even further by replacing some of the sugar with a stevia blend. Of course, healthy all depends on your dietary needs! So make the changes that make sense for you.
Debra says
Can I use all purpose flour instead of wheat flour
Sarah Pilley says
Hi! You can use all purpose flour, and you do not need to adjust any of the other ingredients. I hope you enjoy them
Debra says
Can I use all purpose flour
Marjory Pilley says
Yes! All-purpose flour can be used I. This recipe.
Claudia says
Outstanding one look at that yummy muffin and I was drooling all over my keyboard..I am a huge pumpkin fan perfect...
Marjory Pilley says
I hope you enjoy them!
Katie says
Love that these are a healthier option than your typical muffins! They were still devoured like normal.
Marjory Pilley says
Thanks so much for your feedback!
Pat says
I forgot the sugar. What should I do. The aren’t super sweet because of the chocolate chips
Marjory says
Hi! Here are some ideas for a topping: sprinkle powdered sugar on top, make a cream cheese frosting or make an easy orange drizzle by combining powdered sugar, and orange juice.
Paige says
I have made these twice now, and my family loves them! I used regular white whole wheat flour instead of whole wheat pastry flour, and regular plain yogurt instead of greek, because that is what I had on hand. I also reduced the sugar to 1/2 cup. Absolutely delicious, and I love that they are healthier than most muffin recipes. Thanks so much for the recipe, it is a keeper!
Marjory says
Thanks so much for your tips and comment! I'm so glad you enjoyed them!
Sarah says
I had high hopes for these muffins but they did not work out. Even my pickiest eater wouldn't have more than a taste. Maybe my pumpkin was too watery? I didn't add the extra milk just in case. Disappointing.
Marjory says
I'm so sorry! What was the problem?
Jenna says
Can I use regular white flour or almond flour?
Marjory says
Hi! Unbleached or bleached all purpose flour will definitely work. I've never tried almond flour and additional binding may be needed, such as adding another egg. If you try it, I'd love to know how it turns out!
Laura bourdeau says
If I want to make mini muffins - should I just half the recipe?
Marjory says
Hi! You can use the same recipe just use mini muffin tins and check after 20 minutes. They will cook faster. If you decide to half the recipe, still use 1 egg. I hope you enjoy them!
Susan Funk says
Delicious and very moist! I substituted all purpose flour for the whole wheat pastry flour and almond milk for skim milk and sour cream for the Greek yogurt…very good!
J Clark says
What is the nutritional value of each muffin?
Marjory says
Hi! I'm so sorry but we don't currently offer nutritional information on the site.
Kat says
These muffins were absolute delicious. The kids and hubby couldn't even tell there was pumpkin in there - they thought I was crazy for making cupcakes for breakfast (but didn't complain about it - they just asked for seconds!) This recipe is definitely a keeper.
Marjory says
I am so happy you enjoyed them! Thanks so much for your feedback. Made my day. 🙂
Kirsten/ComfortablyDomestic says
I like to toss a few chocolate chips into my pumpkin muffins, but a chocolate pumpkin muffins sounds even more delicious! Adding yogurt to muffins gives such a great texture.
Kim Beaulieu says
I'm such a chocolate fanatic so these are calling my name. Nothing better than a big fluffy muffin in the morning. These look seriously yummy!
Heather | All Roads Lead to the Kitchen says
I'm loving the addition of Greek yogurt, I bet it makes them so incredibly moist! Plus, chocolate and pumpkin, yes please.
Aly ~ Cooking In Stilettos says
I am a huge fan of Greek yogurt in baking and these muffins need to be made for brunch this weekend. Love it!
Erin @ Texanerin Baking says
I love that these are whole wheat! 🙂 And the Greek yogurt addition must be so yummy. They look nice and moist and I bet so full of flavor!
Renee - Kudos Kitchen says
I love that you've added Greek yogurt into these delicious and decadent looking muffins. The look so moist and chocolaty!
Lora says
How nice, Marjorie! It's great you used whole-wheat pastry flour. Such a great way to make decadent muffins a little bit better for you!
Lauren Kelly Nutrition says
Chocolate + Pumpkin = Heaven! I love these ingredients, these muffins look delicious!
The Food Hunter says
they look absolutely irresistible!
Stephanie says
Wow. These look much to rich and delicious to be healthy! Good job 🙂