Healthy Pumpkin Chocolate Chip Muffins

A hand holding a fluffy and soft pumpkin chocolate chip muffin

With just the right balance of pumpkin spice and chocolate chips, these Pumpkin Chocolate Chip Muffins make a great healthy breakfast, snack, or dessert. They are moist, soft and fluffy. They are also Paleo, Gluten free, Dairy free, and Keto compliant.


Although fall isn’t for another two weeks, I am already so ready for all the fall things. Pumpkin spices, baked apples, cozy sweater. Despite that It still feels like in the middle of summer here in Charlotte, I have already been bringing out all the fall recipes like:


1. Gooey Healthy Pumpkin brownies

2. Apple Pie French Toast Casserole 

3. White Bean Chicken Chili


Why do I love these Healthy Pumpkin Muffins


Nine pumpkin chocolate chip muffins lined up on a cooling rack.


Pumpkin season, Halloween, followed by the holidays. Sometimes it can seem like too much indulgence on sweets. But  these healthy Pumpkin Muffins are just the best holiday recipes that are delicious and guilt free.


1. Healthy and Accessible ingredients to make these Pumpkin Muffins

Instead of regular white sugar, I used maple syrup and coconut sugar which are both paleo friendly. Additionally, you can also use Keto compliant sweetener such as stevia, monk fruit extract to make these muffins Keto friendly.

Moreover, I substituted regular flour or wheat flour with almond flour and coconut flour, which makes this pumpkin muffin recipe Paleo, Gluten Free, Grain-free and Keto Friendly.

2. So Easy to Make

Only 2 bowls (or you can use one), you could have the these soft, pumpkin-y, sweet and cozy chocolate chip muffins in 30 minutes.

3. Perfect Breakfast On the Go or Healthy Dessert

These pumpkin muffins are the perfect breakfast grab and go for a busy morning. They are also crazy kids friendly, perfect for the whole family to enjoy.

Add a scoop of ice cream on the warm pumpkin chocolate chip muffin. Then you have the best fall desserts.


How to Make Pumpkin Chocolate Chip Muffins


Check out this videos for how to Make these Healthy and Cozy Pumpkin Chocolate Chip Muffins.




Healthy Pumpkin Muffin Tips

1. Don’t over mix the batter: over-mixing result sin denser muffins

2. Try other Add-ins: you can also add walnuts, pecans, candied ginger, cranberry, or anything that screams fall at you.



How to Serve these Pumpkin Muffins


Two pumpkin chocolate chip muffins stacked on top of each other. The top one has a bite. The texture seems to be moist and fluffy.


There are so many ways you can enjoy these pumpkin chocolate chip muffins. They are perfect for a breakfast on the go, or a healthy dessert. Here are some of my favorite ways to enjoy these muffins:

  1. Top with yogurt and granola
  2. Top with ice cream
  3. Top with almond butter
  4. Make a Muffin bowl with fruits, nuts seeds and coconut flakes


Can I freeze these Pumpkin Muffins


Absolutely! These pumpkin muffins freeze beautifully. Once the muffins cool completely, put the in an air tight container and store in the freezer.

To thaw: Heat it up in the microwave for 20 – 30 seconds. Or until the middle is warm. Don’t over heat it, these muffins will taste stale.


The perfect cozy fall dessert – these pumpkin chocolate chip muffins are moist, soft and fluffy. This pumpkin recipe is not only so cozy and delicious,  it is paleo, gluten free, dairy free and Keto friendly. Even better? They are great for your kiddos and the whole family to enjoy.


Two pumpkin chocolate chip muffins stacked on top of each other. The top one has a bite. The texture seems to be moist and fluffy.


Yield: 9

Healthy Pumpkin Chocolate Chip Muffins (Paleo, Keto, Gluten Free)

A hand holding a fluffy and soft pumpkin chocolate chip muffin

The best pumpkin chocolate chip muffins that are moist, soft and fluffy. This pumpkin recipe is paleo, gluten free, dairy free and refined sugar free.

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


  • 1/2 cup pumpkin puree
  • 2 eggs
  • 1/3 cup almond butter
  • 1/4 cup maple syrup
  • 1/4 cup almond flour
  • 2 tbsp coconut flour
  • 2 tbsp coconut sugar
  • 1/2 tbsp pumpkin spice
  • 1 tsp baking soda
  • 1/2 cup Chocolate Chip (Divided)
  • 1/2 tsp sea salt (on top)


  1. Preheat the oven to 375 degrees F. Grease the muffin pan generously
    with cooking spray or line with paper or silicone muffin liners.
  2. In a medium bowl, combine all the wet ingredients – Eggs, pumpkin puree, almond butter and maple syrup. IN a separate bowl, whisk together the dry ingredients – almond flour, coconut flour, baking soda and pumpkin spice.
  3. Combine the dry and wet ingredients. Stir until combined using a spatula or fork.
  4. Fold in 3/4 of the chocolate chips and a pinch of sea salt.
  5. Use a medium sized scooper or spoon, divide the batter among 9 muffin cups, or 12 for smaller muffins. Sprinkle the rest of the chocolate chips on top.
  6. Bake approximately 25 minutes or until tooth pick come out
  7. Let it cool on a cooling wrack. Sprinkle extra pumpkin spice
    on top (Optional). Enjoy!


Do not over mix the batter. it will result in denser muffins.

Recommended Products

Disclosure: Some of the links in this post are affiliate links. This does not result in any extra cost for you, but it does mean that I make a commission if you click through and make a purchase.

Nutrition Information:



Serving Size:


Amount Per Serving: Calories: 138Total Fat: 8gSaturated Fat: 1gTrans Fat: 0gUnsaturated Fat: 6gCholesterol: 41mgSodium: 159mgCarbohydrates: 14gFiber: 2gSugar: 9gProtein: 5g

The Nutrition Fact Below is specific to the ingredient I choose to use for this recipe, which may vary.


You May Also Like These Fall Recipes:

1. Gooey Healthy Pumpkin Brownies

2. Pumpkin Cookie Ice Cream Sandwich

3. Roasted Apple Brussel Sprouts


A hand holding a fluffy and soft pumpkin chocolate chip muffin. Pinterest Image.

No Comments

Post A Comment

Shuang Shuang

Hi Friends! My name is Shuang Shuang! I love creating healthy, delicious and accessible recipes that can nourish our bodies and improve our mood. Welcome to a Kitchen Sink full of yummy goodies that you’ll want to give a try yourself!
Read More

What's New

A zucchini banana muffin topped with melty chocolate chips. There is a bite in the middle on the top of the 3.
A bowl of fresh ingredients for mango avocado salsa that include fresh mango, avocado, red onion, tomatoes and cilantro.
A bowl of Chinese Garlic Tofu stir fry on a bed of rice. Topped with scallion.