These Healthy Pumpkin Chocolate Chip Muffins are the perfect cozy fall breakfast or snack that you can feel really good about eating. They are made with whole wheat flour, plain Greek yogurt, pumpkin puree, and maple syrup for a muffin that is naturally sweetened, high in fiber, and protein-packed without any refined oil or eggs. They are also naturally egg free making them a great option for anyone with an egg allergy or anyone looking for a more plant-forward recipe.
They come together in one bowl in under 30 minutes and make a perfect meal prep breakfast for the whole week! Looking for another pumpkin muffin to try? These Pumpkin Banana Muffins are another fun fall breakfast or snack.
30 minutes
Minimal prep
Quick Look: Healthy Pumpkin Chocolate chip muffins
- ⏱️ Prep Time: 5 minutes
- 👩🍳 Cook Time: 25 minutes
- 🕖 Total Time: 30 minutes
- 🎃 Servings: 12 servings
- ⚡️ Calories: 163 cal per muffin (according to recipe card)
- 🔥 Cooking Method: Bake in oven at 350F
- 🛒 Main Ingredients: Pumpkin, Greek Yogurt, Flour, Flax Seed
- ⭐️ Difficulty: Extremely easy! Minimal prep and come together in under 30 minutes!
Shannon left this 5 star review ⭐️⭐️⭐️⭐️⭐️
“Just made these with my granddaughter. 10/10. Delicious! Will definitely make again all season!“
Why You’ll love this recipe
- Naturally egg free and can be made dairy free – These are a perfect fall breakfast or snack option for anyone with a dairy or egg allergy or for someone who is just looking for a more plant-forward recipe!
- Healthy ingredients – These muffins are naturally sweetened, high in fiber, and protein packed so you can feel good about starting your day with one of these!
- Make ahead– These will store well at room temperature for up to 2 days or in the fridge for up to one week. You can also freeze for up to 3 months so go ahead and whip up a double batch!
Looking for another pumpkin breakfast to try? Try this Pumpkin Challah French Toast.
What is a flax egg?
A flax egg is a simple egg substitute made by mixing 1 tablespoon of ground flax seed with 3 tablespoons of water and letting it sit for 5-10 minutes until it becomes thick and gel-like. It acts as a binder in baking just like a regular egg. It is a great egg substitute for muffins, quick breads, and pancakes. It also adds a small boost of fiber and omega-3 fatty acids.
Ingredients you’ll Need
Here’s a quick look at the ingredients you need to make these healthy pumpkin chocolate chip muffins. For a full list of ingredients, see the full recipe.
- Ground Flax Seed – mixed with water to make a flax egg which is a great egg alternative
- Pumpkin and Pumpkin Pie Spice – the pumpkin ingredients that bring this recipe to life
- Plain Nonfat Greek Yogurt – swap for plain dairy free yogurt like coconut or almond milk yogurt if you want to make this recipe dairy free
- Maple Syrup – naturally sweetens these muffins
- Whole Wheat Flour – whole wheat flour gives these muffins more fiber and nutrients than all purpose flour while still producing a tender and moist muffin. You can also use white whole wheat flour for a slightly lighter texture and color. All purpose flour works too if that is what you have on hand.
- Semi Sweet Chocolate Chips – I love the combination of chocolate and pumpkin! If you are making this recipe dairy free, make sure to use dairy free chocolate chips.
Looking for another pumpkin and chocolate recipe to make this fall? Try these Chocolate Chip Pumpkin Scones.
How to make these Healthy Pumpkin Chocolate chip muffins
Step 1: Mix ground flax seed with water in a large mixing bowl and let that sit for a couple minutes to thicken. While that thickens, preheat the oven to 350F and line 12 slots of muffin tin with muffin liners.
Step 2: Pour pumpkin puree, greek yogurt and maple syrup into the bowl with the flask and whisk to combine thoroughly.
Step 3: In a separate bowl, mix together whole wheat flour, pumpkin pie spice, baking soda, baking powder and kosher salt. Pour dry ingredients into wet and fold in with a flat spatula. Mix just until the dry ingredients are incorporated with the wet. Overmixing muffin batter develops the gluten in the flour and makes the muffins tough and dense instead of light and fluffy. A few streaks of flour in the batter are fine.
Fold in chocolate chips with a flat spatula.
Step 4: Scoop ¼ cup of batter into each of 12 muffin cups. Top with extra chocolate chips and bake at 350F for 25 minutes.
Mad’s Expert Tips for the Best Healthy Pumpkin Chocolate chip muffins 🎃
- Let the flax egg sit for the full 5-10 minutes. The flax and water mixture needs time to become thick and gel-like before it is added to the batter. Do not rush this step or the muffins may not hold together as well.
- Do not overmix the batter. Stir just until the dry ingredients disappear. Overmixing makes the muffins tough instead of light and fluffy.
- Fill the muffin cups about two thirds full. This gives the muffins room to rise and dome on top without overflowing. Use a cookie scoop for even portions.
- Sprinkle extra chocolate chips on top before baking. This gives the muffins that beautiful bakery-style look with chocolate chips visible on top. Just a few extra chips per muffin makes a big difference.
For another easy pumpkin breakfast recipe, try these Pumpkin Pancakes.
Recipe FAQs
Are these muffins gluten free?
No, this recipe uses whole wheat flour and is not gluten free. For a gluten free version, swap the whole wheat flour for a one to one gluten free flour blend.
Can I use all purpose flour instead of whole wheat?
Yes! All purpose flour works well in this recipe. The muffins will be slightly lighter in color and texture. You can also use white whole wheat flour for a middle ground between whole wheat and all purpose.
Can I use a regular egg instead of a flax egg?
Yes! If you do not need these to be egg free, you can substitute one large egg for the flax egg. The texture will be very similar.
How do I store these pumpkin muffins?
Store in an airtight container at room temperature for up to 2 days or in the fridge for up to one week. These muffins also freeze great for up to 3 months. Thaw at room temperature or in the fridge overnight.
Storage and Freezing
Place in an airtight container at room temperature for up to 2 days or in the fridge for up to one week. These muffins also freeze great for up to 3 months. Thaw at room temperature or in the fridge overnight.
Other Yummy Pumpkin spice Breakfast Recipes
You can find the full recipe below. If you make this recipe, please rate and review it in the comments, or share it with me on Instagram!
Email Recipe for Later
Recipe
Healthy Pumpkin Chocolate Chip Muffins
Ingredients
- 2 tbsp ground flax seed
- ¼ cup water
- 1 cup pumpkin puree just pumpkin as the ingredient
- ½ cup plain nonfat greek yogurt
- ½ cup maple syrup
- 1 ½ cups whole wheat flour
- 2 tsp pumpkin pie spice
- 1 tsp baking soda
- 1 tsp baking powder
- ½ tsp kosher salt
- ¾ cup semi sweet chocolate chips + more for topping
Instructions
- Mix ground flax seed with water in a large mixing bowl and let that sit for a couple minutes to thicken. While that thickens, preheat the oven to 350F and line 12 slots of muffin tin with muffin liners
- Pour pumpkin puree, greek yogurt and maple syrup into the bowl with the flask and whisk to combine thoroughly.
- In a separate bowl, mix together whole wheat flour, pumpkin pie spice, baking soda, baking powder and kosher salt. Pour dry ingredients into wet and fold in with a flat spatula.
- Fold in chocolate chips with a flat spatula.
- Scoop ¼ cup of batter into each of 12 muffin cups. Top with extra chocolate chips and bake at 350F for 25 minutes.
- Allow muffins to cool completely before enjoying.
Nutrition Information
This website provides approximate nutrition information for convenience and as a courtesy only. Nutrition data is gathered primarily from the USDA Food Composition Database, whenever available, or otherwise other online calculators.
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