Whole Wheat Mini Pumpkin Muffins

These adorable mini 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.

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!

Do you think mini muffins are 100x better than regular size muffins? I certainly do! Today’s mini pumpkin muffins have the same great flavor as my pumpkin bread, made into itty bitty, lightened up bite-sized muffins. You won’t be able to stop after just one!

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
  • Loaded with mini chocolate chips
  • Only 60 calories each

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!

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: Pumpkin adds flavor and incredible moisture. Make sure to use real pumpkin puree (not pumpkin pie filling).
  • 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. Don’t leave it out!
  • Milk: Milk adds moisture.
  • Chocolate Chips: Mini chocolate chips are best. You get many more in each muffin! Use any leftover in mini chocolate chip muffins.

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!

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

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!

More Favorite Pumpkin Recipes


Whole Wheat Mini Pumpkin Muffins

  • Author: Sally
  • Prep Time: 20 minutes
  • Cook Time: 12 minutes
  • Total Time: 35 minutes
  • Yield: 36 mini muffins
  • 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 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: Instead of pumpkin pie spice, you can use 1/4 teaspoon each of ground nutmeg, ground ginger, ground cloves, and ground allspice. Sometimes I use closer to 1 and 1/4 teaspoons pumpkin pie spice. I like a lot of spice flavor!
  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

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!

Pumpkin chocolate chip muffins made with whole wheat flour and only 60 calories each!


  1. Averie @ Averie Cooks says:

    Good luck at the Mall of America! I grew up in MN before moving to San Diego (can’t wait for that tour stop!) and used to work at that mall in h.s….the memories. Have fun!!!

    These are just tooooo adorable. Mini food just tastes better, period. And it’s healthy. Dangerous, seriously could pop 6 of them in about 6 seconds!

  2. Andrea | Cooking with a Wallflower says:

    I love that these pumpkin muffins are whole wheat and mini! That way I won’t feel guilty about indulging in these plus I get to have more than one. Breakfast set for next week!

  3. How cute are these! I love mini desserts. But you are right, they are dangerous, you eat a looot more then you’d think. They sound delicious as well.

  4. Heather | Delicious Not Gorgeous says:

    I’ve been passing Starbucks a lot this week, and have already succumbed once to their pumpkin cream cheese muffin. But it’s fairly caloric, and it’s so high in sugar! So motivated to try these ones instead (: 

  5. I totally think minis are more fun! These look super delicious, Sally!

  6. I’m with you on the mini muffin love. My kids get mini pumpkin muffins that my mother-in-law bakes them, and they love them. I think the size has as much to do with it as the taste!
    I like yours better, though, because they have chocolate chips. Chocolate chips make everything better!

  7. Rachel @the dessert chronicles says:

    I LOVE mini muffins!! I totally agree it is just more fun to be able to eat a handful in a sitting and not feel too bad about it. Definitely no judgement here if you eat more than just a handful though! These look amazing, Sally!

  8. Katrina @ Warm Vanilla Sugar says:

    These little muffins look so flavourful! So delicious!

  9. These look like a must-try! When I bake with pumpkin, it just makes everything feel a lot more like fall. And I’ve got a huge can of the stuff in the fridge 🙂 

  10. This is similar to the recipe I have adapted from a few places and it is sooo good. I use maple syrup for the sweetener and it goes so well with the pumpkin! These are perfect to go in the freezer for lunchboxes!

  11. Sally, I totally agree with you on the entire subject of mini muffins with mini chocolate chips. I think minituare rocks, be it muffins or people (I might be a little prejudiced there being 5′ 2″ myself).  I always shayed away from the baking recipes using greater percentage of the whole wheat flour.  But this muffins look very light and airy.  And of course the caloric count does not hurt either, considering the chocolate chips (oh, those little devils!).  I am very curious to try them.

  12. Linda @ Today She Loves says:

    Yum, I’ve been looking for an alternate to pop tarts for breakfast. Could I use only almond flour on these muffins or will texture change? 

    1. The texture will definitely change. I don’t recommend it!

  13. Perfect breakfast right here! Can’t wait to make them 🙂

  14. Lucia @ The Foodwright says:

    Just last night I was wanting to make some whole wheat pumpkin muffins, but I didn’t have any recipes & didn’t feel like experimenting, haha! Can’t wait to try these!! They look so good. 

  15. Hi Sally! Huge fan and I’m so hoping I can venture to somewhere nearby Montreal to meet you! How long should I bake them if I want to make them using a regular-sized muffin pan?

    1. Hi Samantha- see recipe notes. I would love to visit Montreal someday. Not sure it will be on this book tour though!

  16. Could I double up the recipe? Would rather use a whole can of pumpkin and bag of mini choc chops

  17. Megan @ Pastry School Dropout says:

    How would you adjust the time/temperature if you made these into regular-sized muffins?

    1. Megan, see recipe notes. 🙂

      1. Megan @ Pastry School Dropout says:

        My bad! I read till #4 and thought that was all. Mommy brain going on right now…

  18. Patricia Ribler says:

    Just made these and they are fantastic! I make a lot of whole wheat muffins but these really don’t taste like whole wheat, they are so good! I subbed fresh cranberries for the chocolate chips because pumpkin + cranberry = fall goodness! Even my 3 year old loves them! Thanks for another great recipe! 

    1. Glad you already made them Patricia! I know, aren’t they great? I’ll try them with fresh cranberries next!

  19. Elaine @ FoodParsed says:

    These muffins are so cute! I love the artfully staged muffin stacks.

  20. Oh they look so good! 🙂 

  21. I made these this afternoon for my kids and they are very yummy! I will be making these again for sure. 

  22. You should check out Crêpes ‘n Crêpes in Denver at Cherry Creek, was one of my favorite places when I lived there.


    1. Thank you for the suggestion!

  23. I don’t have any whole wheat flour. Can I substitute with all purpose?

  24. It’s too bad you don’t have it planned to visit Ottawa, Canada or even Montreal. I’m planning to make these to use up my leftover pumpkin puree from Thanksgiving. I hear yours is in November?

  25. Bet @ Bet On Dinner says:

    I made the full-size muffins and they have been devoured! My favorite treat at a nearby bakery is a pumpkin with white chocolate chips – as soon as I get my hands on some white chocolate chips, I’m going to throw them in and save myself $2.50! :o)

  26. These muffins just became my new favorite whole wheat treat! I baked them in a traditional muffin tin, 5 minutes on 425, 13 minutes on 350. They cooked through perfectly, had a great dome on top, and were extremely moist! I also used coconut oil in place of butter and am very pleased with the final product. Thanks for another great recipe! 

  27. I was just wondering which kind of whole wheat flour do you recommend?

    1. I love King Arthur Flour’s whole wheat.

  28. Heather @ Boston Girl Bakes says:

    Oh my 60 calories!! I’ll just stop counting after two 🙂 These would be dangerous for sure!

  29. Natasha @ Salt and Lavender says:

    Those are so cute. I like the idea of mini muffins better than full-size ones. I never seen to finish full-size ones and so I avoid buying or making them! Pinned!

  30. Broke out my mini muffin pan for the first time for this recipe. Even though I was missing ginger (and pumpkin pie spice), they turned out great!! And mini muffins are just too stinkin’ cute! 

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