Pumpkin Chocolate Chip Mini Muffins

5 stars average

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These bite-sized pumpkin chocolate chip mini muffins are made with whole grains and warm fall spices.

Mini Pumpkin Chocolate Chip Muffins in a muffin tin

I’ll be the first to admit that I prefer to cook over bake but when the temps start to drop and the leaves start to fall, I find myself gravitating more and more to the kitchen where I can warm up by the oven.


My boys love anything made with pumpkin so I knew right away these pumpkin chocolate chip mini muffins would be a huge hit. In fact, we enjoy pumpkin all year round in oatmeal, smoothies, pancakes and more.

Pumpkin Chocolate Chip Mini Muffins

Add chocolate to the mix? Well, that’s a no brainer. They’re going to love it.

Liz Making Mini Pumpkin Chocolate Chip Muffins

The secret to my healthy pumpkin muffins is the addition Stonyfield organic plain whole milk yogurt.

Liz Making Pumpkin Muffins with Yogurt

In fact, baking with yogurt is not only a great way to cut down on total fat but it keeps the baked goods light and moist.

Chocolate Chip Pumpkin Mini Muffins Recipe

Ideal for freezing, I love whipping up a double batch of these mini muffins and stashing half of them in the freezer to use at a later time. Pro Tip: If you individually wrap them in plastic wrap, you can pull them out one at a time as needed.


An ideal option for school snack, I love pairing these pumpkin mini muffins with a Stonyfield yogurt tube. Both are portable and nut-free making them ideal for the classroom.

pumpkin mini muffins

What are your favorite healthy snacks for little ones? I’d love to hear from you!

No forks required.

pumpkin mini muffins

Pumpkin Chocolate Chip Mini Muffins

5 stars average
These bite-sized pumpkin chocolate chip mini muffins are not only tasty but made with whole grains and warm fall spices. Perfect for snacks!
PREP: 15 minutes
COOK: 12 minutes
TOTAL: 27 minutes



  • Preheat oven to 350 degrees and have a non-stick mini muffin pan ready to use.
  • In a medium bowl, whisk together dry ingredients: flour through cloves; set aside.
  • Using a stand mixer, blend together wet ingredients (pumpkin through vanilla) using the lowest setting to ensure you don’t get splattered. Move the speed up a notch to medium and slowly add in the dry ingredients, about 1/2 a cup at a time, until they’ve all been added.
  • Turn off mixer and scrape down the sides of the bowl with rubber spatula. Turn the mixer back on to low speed and carefully stir in the chocolate chips. Turn off as soon as they’ve all been added. Remove bowl from the stand mixer.
  • Using a small cookie scoop, carefully scoop out 48 muffins into the muffin pan. Bake until a toothpick comes out clear, about 10-13 minutes. Let cool on a cooling rack at least 15 minutes before removing from pan. 

Last Step:

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Serving: 2muffinsCalories: 133kcalCarbohydrates: 17gProtein: 2gFat: 6gSaturated Fat: 4gCholesterol: 17mgSodium: 87mgPotassium: 129mgFiber: 1gSugar: 9gVitamin A: 1630IUVitamin C: 0.5mgCalcium: 48mgIron: 0.7mg
Did You Make This Recipe?Post a pic and mention @thelemonbowl or tag #thelemonbowl!

Disclosure: I am honored to be a Stonyfield Brand Ambassador. Thank you for supporting the brands that make The Lemon Bowl possible. All thoughts are my own.

Looking for more delicious and easy breakfast ideas? Head over to my Pinterest Board for more!

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8 responses to “Pumpkin Chocolate Chip Mini Muffins”

  1. L.A. Avatar

    This looks like a great recipe. Would it be okay for me to use almond flour in this recipe?…and would I use the same amount…2 cups?

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      You should be able to swap them without any issues!

  2. 2pots2cook Avatar

    Ha ha ha, my son does exactly the same thing :-) Keeping to make my boy enjoy ! Thank you Liz !

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      hehe – enjoy!

  3. Marpy Avatar

    Can I make these in a regular-sized muffin tins?

    1. Liz DellaCroce Avatar
      Liz DellaCroce

      Absolutely!! :)

      1. Alissa Onigman Avatar
        Alissa Onigman

        What is the baking time for regular muffin size treat

        1. Liz DellaCroce Avatar
          Liz DellaCroce

          Use this recipe for regular size! https://thelemonbowl.com/healthy-pumpkin-muffins/