healthy chocolate chip pumpkin muffins
Snacks,  Breakfast,  Desserts

Healthy Pumpkin Muffins (Extra Fluffy)

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These Healthy Pumpkin Muffins have no refined sugars or flours! Instead, they are made with almond flour, whole-wheat flour, honey, and coconut sugar. You only need one bowl to make them! Pop these muffins in the oven and your house will smell like a cozy fall day.

Easy Healthy Pumpkin Muffin Recipe

These Healthy Pumpkin Muffins pair perfectly with a cup of coffee or tea. They’re also great if you are looking for an easy snack or on-the-go healthy breakfast!

They are the perfect addition to your portable snack arsenal. And if you have little ones, you can use these muffins as a healthy snack alternative in comparison to those prepackaged mini muffins. You know… the ones that are easy, BUT loaded with processed sugars and other scary preservatives….eeek. This recipe will save your kiddos from going crazy off a sugar high too… DOUBLE BONUS!

The Perfect Healthy Flour Combination

Recipes that call for ALL whole-wheat flour seem to have the same taste…CARDBOARD. Not particularly something you want to sink your teeth into. But, you’re trying to be healthy! Looks like you’ll just have to suffer and eat those dry muffins with a gallon of milk in hand to get them down your throat. JUST KIDDING! I have some encouraging news my friends because I have a recipe for you that is HEALTHY and DOESN’T taste like cardboard! HOORAY! Like I always say, healthy doesn’t have to taste bland or dry

These Healthy Pumpkin Muffins are made with THE PERFECT flour combination! Instead of getting that dry, cardboard taste from using all whole-wheat flour, this recipe calls for ⅔ cup almond flour and only ⅓ cup whole-wheat flour. 

pumpkin muffins

Almond flour:

The benefits of almond flour aren’t as secret as you would think. Almonds are amazing for you (read about nuts and what key nutrients are found in them), so naturally almond flour is amazing for you! Packed with calcium, healthy fats, and those lovely Omega 3’s! These nutrients help your body regulate blood sugar, relieve stress and support a healthy gut!

Whole-wheat flour:

Now if you really want these muffins to be the fluffiest guys on the block, my suggestion is to use homemade whole-wheat flour. I know that makes me sound like I live in the 1800’s, but trust me it’s super simple! Just head over to my How to Make Homemade Flour post. It’s only 3 steps, one ingredient and takes just 5 minutes or less!

If you only have store-bought whole-wheat flour on hand, don’t worry! I have tried this recipe with King Arthur white whole-wheat flour and they still turn out fluffy and delicious!  Plus using any type of whole-wheat flour adds WAY MORE health benefits than highly processed white flour!

chocolate chip pumpkin muffins

In case you’re curious as to why Whole-wheat flour is thaaat much better, here are some facts. Whole-wheat flour is rich in fiber, vitamins, folate, and so much more! These nutrients make whole-wheat flour amazing for gut health, controlling blood sugar levels, preventing disease, and aiding in weight-loss management. You can read more about the benefits of whole-wheat flour here. 

Another fabulous resource, if you are wanting to learn more about whole-grains, is the book, Cooking With Ancient Grains, by Laura B. McBride. The type of whole-wheat berries you should purchase for this recipe are Organic Hard White Wheat.

Comment below if you are interested in learning more about making homemade flour, the health benefits, and cost-efficiency and I will for sure write a post about it! And it will give me a hint if you are actually reading this 😉

Secretly Healthy Sweeteners

Coconut Sugar:

This sweet stuff is loaded with magnesium, potassium, electrolytes and so much more! Coconut sugar is a natural sweetener that doesn’t spike your blood sugar! I go in-depth about coconut sugar in my 6 Low Cost Superfoods post. Definitely a good read if you are looking for guidance on what superfoods to buy without breaking the bank!


Such an amazing process that goes behind honey. Bees. Flowers. Pollination. Honeycombs. God thought it all out. It blows my mind how such tiny little creatures like bees know how to create beautiful and intricate honeycombs and produce honey. And to top it all off, the stuff is literally liquid gold! Honey is filled with antioxidants that can give you glowing, dewy skin, and shiny, hydrated hair. Something regular white table sugar cannot give you! Read all about the benefits of honey here. 

Grass-Fed Butter Benefits 

Yes, I will allow you to use regular butter if you don’t have grass-fed. 😉 However, I highly recommend making the switch to grass-fed butter. I was always afraid of buying grass-fed butter because I thought it would cost me an arm and a leg, but in reality, the price of grass-fed butter shocked me! It’s only around $3.69 for 8 oz. (which is about 2 sticks of butter). The beauty of this butter is that a little goes a LONG WAY. It’s so rich, creamy, and flavorful! And that’s only the beginning…

Health benefits of grass-fed butter vs. regular butter:

  • More Omega 3’s (Omega 3’s are not produced in the body so it is essential we have a diet rich in them).
  • 500% more Long Chain Omega 6 fatty acids (CLA)- can prevent cancer, help with inflammation, boost your immune system and fight disease.
  • Higher Fat-Soluble Vitamins such as Vitamin A, D, K, and E.

I am a visual learner, so here is an aesthetically pleasing picture of the health benefits of grass-fed butter.

Ingredients for Whole Wheat Pumpkin Muffins

We can’t forget the other secret ingredients in these muffins! Pumpkin pie spice and of course, pumpkin!

Pumpkin Pie Spice: 

Spices aren’t only flavor enhancers, they are powerful in the world of healthy cooking and baking! Highly overlooked too… poor guys. The cozy spices found in pumpkin pie spice are warming to the soul and valuable to the body and how it functions. 


Has the ability to boost your metabolism, curve sugar cravings, and ward off diseases. Cinnamon is an absolute must, especially because it’s apart of the 6 Low Cost Superfoods that can change your life! 


Another key spice found in this fall spice ensemble. Feeling under the weather? Becoming paranoid as everyone around you sniffles and coughs? Well, grab some ginger because it’s an immunity booster! It also has anti-inflammatory properties that can help with acne, muscle soreness, and bloating.

Cloves and Nutmeg

The final ingredients that contribute to this spice family. Both cloves and nutmeg are high in antioxidants and have the ability to relieve stress and kill off bacteria (protecting you all the more from those snifflers).


I go into detail about the benefits of pumpkin in my Secretly Healthy Fudge Brownie Recipe! Check it out, pop some healthy brownies in the oven and get to reading!

Healthy Pumpkin Chocolate Chip Muffins ready for the oven!

If you made it to the end of this post, give yourself a high-five because you just learned a TON about how these Healthy Pumpkin Muffins can positively impact your health! Whoooop Whooooop!

Goodbye prepackaged, sugar bomb, preservative packed muffins, hello Secretly Healthy Muffins!

Like I said, comment below if you are interested in learning more about making homemade flour, its health benefits, cost-efficiency, etc. and I will be sure to write a post about it!


healthy chocolate chip pumpkin muffins pintrest
Yield: 9 Large Muffins

Healthy Pumpkin Muffins (Whole Wheat)

healthy chocolate chip pumpkin muffins

Healthy Chocolate Chip Pumpkin Muffins with no refined sugars or flours! Made with almond flour, whole-wheat flour, honey, and coconut sugar!

Prep Time 10 minutes
Cook Time 25 minutes
Total Time 35 minutes


Wet Ingredients

Dry Ingredients


1. Preheat oven to 350 F. Place 9 muffin liners in a muffin tin (or grease with coconut oil).

2. In a medium bowl, combine eggs, honey, coconut sugar, melted butter, and pumpkin and whisk until smooth. 

3. To the batter, add in almond flour, whole-wheat flour, salt, pumpkin pie spice, baking soda, and baking powder. Mix until combined.

4. Fold in chocolate chips

5. Pour an even amount of batter into each muffin cup.

6. Put in the oven and bake at 350 F. for 25-30 minutes.

7. Devour! (Or store in an airtight container in the fridge for up to 5 days. Freeze for up to 3 months!)


-If you want to make these mini muffins, just adjust the bake time to 10-15 minutes.

-Make sure you use PURE PUMPKIN puree, NOT canned pumpkin pie mix.

-Here are the whole-wheat berries/groats I love to use when making homemade flour: Hard White Wheat Groats.

*Give these Healthy Chocolate Chip Pumpkin Muffins a try and be sure to tag us on Instagram! @secretlyhealthyhome

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Nutrition Information:



Amount Per Serving: Calories: 185Total Fat: 9.1gCarbohydrates: 26.7gProtein: 3.7g

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