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These adorable mini whole wheat pumpkin muffins are made with whole wheat flour, real pumpkin puree, mini chocolate chips, and lots of cozy pumpkin spice. They’re full of flavor, incredibly moist, and only 60 calories each! Follow my recipe notes to make these as regular size muffins, too.

mini pumpkin chocolate chip muffins

Do you think mini muffins are 100x better than regular size muffins? Today’s mini pumpkin muffins have the same great flavor as these regular pumpkin muffins and my pumpkin bread, but made into itty bitty and slightly lightened up muffins.

These Whole Wheat Mini Pumpkin Muffins Are:

  • Wholesome and satisfying
  • Moist and flavorful
  • Simple to make—no mixer required
  • Great for breakfast, a snack, or dessert
  • Perfectly pumpkin spiced and you can use this pumpkin pie spice recipe
  • Loaded with mini chocolate chips
  • Only 60 calories each
mini pumpkin chocolate chip muffins on an orange and white plate

Whole Wheat Pumpkin Muffins – Ingredients

There’s so much fall flavor in each bite of today’s mini muffins. Here’s what you need:

  • Whole Wheat Flour: We use wholesome and hearty whole wheat flour as the base of these muffins.
  • Baking Powder & Baking Soda: These leaveners help the muffins rise.
  • Cinnamon & Pumpkin Pie Spice: I like to use a blend of these cozy spices for mega fall flavor. Instead of pumpkin pie spice, you can use 1/4 teaspoon each of ground nutmeg, ground ginger, ground cloves, and ground allspice.
  • Salt & Vanilla Extract: Both add flavor. Try using homemade vanilla extract.
  • Eggs: Eggs add moisture and bind the ingredients together.
  • Brown Sugar: A little brown sugar sweetens these muffins.
  • Pumpkin: 1 cup (about 225g) of pumpkin puree adds flavor and incredible moisture. If you have extra to use up, here’s what you can make with leftover pumpkin puree!
  • Butter: A touch of melted butter helps make the muffins taste good—no rubbery or dry muffins today. We use just enough butter to give the muffins a rich, tender texture but still keep them on the lighter side.
  • Milk: Milk adds moisture.
  • Chocolate Chips: Mini chocolate chips are best because you get many more in each tiny muffin. Use any leftover in mini chocolate chip muffins.
mini pumpkin chocolate chip muffins

Nutrition Facts

I don’t typically post nutritional facts for my recipe, but I was curious about these and thought you would be, too.

Here’s the calorie breakdown of the full mini muffin recipe:

  • Whole wheat flour = 710
  • Eggs = 140
  • Lightly packed brown sugar = 230
  • Pumpkin = 80
  • Melted butter = 505
  • Unsweetened almond milk (I used Almond Breeze brand) = 10
  • Spices + vanilla = 22
  • Mini chocolate chips = 550

Divided by 36 mini muffins = 60 calories each

mini pumpkin chocolate chip muffins

For another mini-breakfast favorite, try my mini french toast bites next. Fun to make and even more fun to eat!

More Favorite Pumpkin Recipes

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mini pumpkin chocolate chip muffins on an orange and white plate

Whole Wheat Mini Pumpkin Muffins

  • Author: Sally
  • Prep Time: 20 minutes
  • Cook Time: 12 minutes
  • Total Time: 35 minutes
  • Yield: 36 mini muffins 1x
  • Category: Muffins
  • Method: Baking
  • Cuisine: American


Here’s my simple recipe for whole wheat mini pumpkin muffins. They’re only 60 calories each!


  • 1 and 3/4 cups (220g) whole wheat flour* (spoon & leveled)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • 1/2 teaspoon salt
  • 1 teaspoon ground cinnamon
  • 1 teaspoon store-bought or homemade pumpkin pie spice*
  • 2 large eggs, at room temperature
  • 1/2 cup (95g) lightly packed brown sugar
  • 1 cup (228g) pumpkin puree (not pumpkin pie filling)
  • 1/3 cup (72g) unsalted butter, melted and slightly cooled*
  • 1 teaspoon pure vanilla extract
  • 1/3 cup (80ml) milk (I use almond milk; any milk is OK)
  • 1/2 cup (90g) mini chocolate chips*


  1. Preheat oven to 350°F (177°C). Grease/spray two mini muffin pans with nonstick cooking spray. This recipe makes around 36 muffins, so you will only use half of the 2nd pan. If using mini liners, grease/spray them with cooking spray. Set pans aside.
  2. In a large bowl, whisk the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice together. Set aside. In a medium bowl, whisk the eggs, brown sugar, pumpkin puree, melted butter, vanilla, and milk together until combined. Pour the wet ingredients into the dry ingredients, stir a few times, then add the mini chocolate chips. Fold everything together gently just until combined.
  3. Fill muffin cups around 3/4 – all the way full. Go for about 1 heaping Tablespoon of batter per muffin. Bake for 12-14 minutes or until a toothpick inserted into the center comes out clean. If your oven has hot spots, be sure to rotate the pans during bake time. My muffins took 12 minutes. Remove pans from the oven. Allow muffins to slightly cool before enjoying.


  1. Make Ahead & Freezing Instructions: Muffins stay fresh in an airtight container at room temperature or in the refrigerator for 5-7 days. Muffins can be frozen up to 3 months. Thaw overnight in the refrigerator and warm to your liking before serving.
  2. Flour: You can also use white whole wheat flour or all-purpose flour. Or a mix of whole wheat and all-purpose.
  3. Pumpkin Pie Spice: You can find pumpkin pie spice in the baking aisle of most grocery stores or make your own homemade pumpkin pie spice. If you don’t have either and want to use individual spices, use 1/4 teaspoon each: ground ginger, ground nutmeg, ground cloves, and ground allspice. This is in addition to the 1 teaspoon of cinnamon—you will still add that.
  4. Butter: I do not recommend leaving out the butter. This is what makes these muffins tender and similar to the texture of higher calorie pumpkin muffins. You can use oil or melted coconut oil in its place. Do not sub applesauce; the muffins will have a rubbery texture.
  5. Chocolate Chips: Mini chocolate chips are best. You get many more in each muffin which makes them taste so good. Feel free to increase mini chocolate chips to 2/3 cup (I’ve done that– so good!). I do not recommend regular size.
  6. Regular Size Muffins: Makes 12-14 regular size muffins. Bake for 5 minutes at 425°F (218°C), then keeping the muffins in the oven, reduce temperature to 350°F (177°C) and bake for an additional 16 minutes or until a toothpick inserted in the center comes out clean. The total times these muffins take in the oven is about 20-21 minutes, give or take. The initial high temperature helps create tall muffin tops. You’ll love it!

Keywords: mini pumpkin muffins, whole wheat pumpkin muffins

overhead image of mini pumpkin chocolate chip muffins

Reader Questions and Reviews

  1. This is my 6 year old daughter’s favorite breakfast food, and it has been since we started baking them 4 years ago when she was 2. I appreciate that they use pumpkin, whole wheat, and we half the sugar so these muffins are healthy, or at least healthier than most other baked goods. We freeze most of them (we made minis when she was little but now we do full size) and grab one out the night before to thaw in time for breakfast. All of Sally’s recipes are amazing but this is a winner for us and a regular in our kitchen!

  2. Great flavor. I found them to be a bit dry. Maybe add a bit of sour cream or applesauce

  3. I followed the recipe exactly but these just weren’t sweet enough and a bit dry. Next time I’m going to sub some regular flour in and add 1/4 c more sugar. Also more pumpkin spice. Less healthy, sure, but the whole wheat makes them filling enough that I am not inclined to eat so many.

  4. Can I use white whole wheat flour? Maybe a combination of coconut oil and butter in place of all the butter?

    1. Hi Sheryl, You can use white whole wheat flour. And a mix of butter and melted coconut oil would be fine. Happy baking!

  5. Just made these this morning in a regular size muffin pan and they came out PERFECTLY! I’m not a fan of pumpkin and chocolate together, so I added walnuts and a light sprinkle of a superseed mix (pumpkin, flax, chia, sunflower, hemp seeds) on top. The nuts and seeds on top adds some extra crunch, and enhances the appearance. Will definitely be making again!

  6. These turned out fantastic! The whole wheat flour gives them a nice nutty taste.

  7. I just made these this morning and they were a hit! Literally half of them were eaten within 10 minutes of coming out of the oven.
    Just a fun side note, my kids got an easy bake oven for Christmas and were eager to try their muffin pan that goes with it. It fit maybe 1 tsp of batter in each cup and baked for 9 minutes. Worked like a charm. Just thought I’d add that for anybody else with aspiring bakers at home!

  8. Sally’s recipes never disappoint. I was surprised at how light the mixture was going into my muffin cups, with it being whole wheat flour. I made sure to not pack the flour down when measuring, and I also added a heaping cup of pumpkin puree to add a little more moisture. They were perfect, and my kids love them!

  9. I made these with 1 cup of mashed bananas instead of pumpkin and omitted the pumpkin spice. They were perfect; not too sweet and even semi-healthy with the whole wheat flour. I’ll try them with the pumpkin next month (Sept) because I’m told I’m too pumpkin crazy and I’ve limited myself to pumpkin baking from Sept to Nov only.

  10. So delicious! I made regular sized muffins, added a squeeze of sour cream, and used cinnamon chips instead of chocolate chips. They turned out so wonderfully moist. Perfect especially for fall!!

  11. Good evening! I was wondering if I could use oat bran in place of the whole wheat flour? If not, do you have an oat bran muffin recipe? That would be great. Thank you! By the way, these muffins were great!

    1. Hi Sarah, we haven’t tested these muffins with oat bran so we’re unsure of the results. We’d caution against it, as oat bran has very different baking properties and will soak up liquids differently than whole wheat or all-purpose flour. We don’t have an oat bran muffin at this time, but let us know if you find one you love!

    1. Hi Carol, absolutely. Since the mini muffins are so small, you might prefer to use dried cranberries. If using fresh, chop them up a bit before adding to the batter. Keep total amount of add-ins to 1/2 cup. Enjoy!

  12. Love this ”
    Whole Wheat Mini Pumpkin Muffins”, these muffins seems so delicious, will definitely gonna try these. Thanks for sharing with us .

      1. Hi Farah, We haven’t tested it but it you wish to, we don’t recommend substituting more than one half of a cup of wheat bran. Keep in mind that they do have different baking properties, so expect the muffins to have a different texture than intended. Let us know if you give it a try!

    1. Hi Michelle, how did you measure your flour? We recommend spooning and leveling (or weight measuring) your flour to ensure that there is not too much in the batter, causing it to dry out the muffins. Also be sure not to over bake, as even just a minute or two longer than needed can dry out baked goods. Hope this helps for next time!

  13. Hi!
    I love your recipes! I’m just shy of 2 cups of pumpkin puree, if I want to double this recipe to use that entire amount, are there any particular tweaks you’d suggest?

    1. Hi Finny! We’re unsure of exactly how you would need to adjust the recipe – best to stick with the amounts as written if possible. Let us know how they turn out!

  14. I made these for those days I don’t want to cook breakfast. Substituted unsweetened apple sauce for the butter and omitted the chocolate chips and they turned out well. Nice pumpkin flavour with a hint of spice. These will be in my regular rotation.

  15. Excellent recipe, the kids and husband loved them. They are not overly sweet, but still very flavourful.

  16. Goodmronig! I am going to make these this morning, and I noticed that the weight advises 220g for 1 and 3/4 cups wheat flour. Is this is an error, or do you all use different calculations than 113g per 1 Cup of wheat flour? Based on some comments from other readers here, I think I will go with 198g, so hopefully that will turn out just right :0). Thanks for all of the recipes on this site – I come here often and have had so many great results! You guys are great!

  17. Hi Sally…I have made these many times in the past…always fabulous!…this time however, instead of Chocolate Chips, I substituted 3/4cup of grated carrot ….also halved the brown sugar….super healthy version and delicious!

  18. My 5 year old Granddaughter loves these mini muffins. Perfect for a school snack! My 1 year old Granddaughter was envious of her sister’s muffins so I made her a batch without chocolate chips. Big hit!

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