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.

mini pumpkin chocolate chip muffins

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

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: 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.

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

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
  • 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

overhead image of mini pumpkin chocolate chip muffins


  1. Is it okay to use whole wheat pastry flour?

    1. Yep! Same amount.

  2. Made these today and my whole family loved them.  They rose much better than my pumpkin muffins usually do though not as smooth on top as yours. My tops are a little bumpy. Very yummy though. Thanks for the recipe. 

  3. Can these be made in a regular size muffin tin as well?

    1. Yep! See my recipe note.

  4. Another great recipe! I made them for the first time last week and I’ve got another batch in the oven right now…so good!

    1. I always find myself doubling this one!! Love having a freezer stash of these!

  5. Made regular muffins and came out to 14. Weren’t super high muffin tops but I could’ve filled them more. Huge hit!!!

    I also pushed in some chocolate chips on the top after spooning in the batter to make them look a little better. They took the full 21 mins and I rotated once in the oven.

    1. I made 12 regular sized muffins, filled almost to the top and they turned out great.

  6. How much will the calories be when I use all purpose flour and skip the chocolate chips?

    1. Hi Julie! I’m unsure. Feel free to use an online calculator.

  7. Ann Bickenheuser says:

    I made the mini pumpkin mffins today. Very yummy and the come out of the pans so easily abd they look perfect.

  8. Hi! I had just about 1 cup of leftover pumpkin from making pancakes this weekend and also needed a healthy snack to send to school with my oldest daughter. Two birds! This recipe is great! I made regular size muffins because I only had regular size chips. It made 13. Both of my girls loved them! They definitely taste healthy (in a good way!) but the chocolate chips make them feel indulgent so it’s a win-win. My oven runs hot so they took 5 minutes at the higher temp and then only 14 minutes at 350 for the regular size muffins. Such an easy recipe that I actually made them while I was on a conference call. HA! Thanks for another winner, Sally!

  9. These are the best pumpkin muffins we’ve ever made! My kids have been eating them for their snack in the afternoons and I can barely keep up with making them! We bake a batch and freeze them to keep us from eating the whole batch in one day 🙂

    1. I’m thrilled that these are such a hit in your home, Irene!

  10. Hi, Sally! Will the texture of the muffins be different if I use all purpose flour? And what if I use margarine instead of butter (I actually don’t want to, but just in case), will the texture be different too?

    1. Hi Tasha! I don’t recommend margarine, but you can use all-purpose flour instead. I do that all the time! Same amount. Muffins taste a little lighter.

  11. Can I use almond flour instead? Also, could I turn these into banana muffins instead of pumpkin?

    1. Hi Heidi! Almond flour won’t soak up enough liquid. I fear the muffins will be too wet and heavy. You can try mashed banana instead of pumpkin, yes!

  12. This is gonna be my next baking to celebrate the weekend coming! I will go for regular muffins, though, as I must admit I don’t have a mini-muffin pan… yet!
    Would you recommend to fill (regular) liners all the way to the top, just like in other recipes of yours for regular muffins?

    1. Hi Gabrielle, see my recipe notes about regular size muffins. Enjoy!

  13. I make muffins regularly to pack in the lunches I bring to work, and I tried this recipe last week. They were delicious! Moist, great pumpkin spice taste, not too sweet but very flavorful, and relatively healthy.

  14. These are the most MOIST and soft muffins I’ve ever made/eaten. I made them normal sized and added frozen cranberries too. Measured by grams provided in recipe. DELICIOUS! ( I rarely review recipes). This will be a go-to.

    1. I’m thrilled you enjoy them so much, Maddison! Thank you for taking the time to leave a review!

  15. 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!

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

  17. 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.

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

    1. Stephanie @ Sally's Baking Addiction says:

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

  19. 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!

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

  21. I haven’t made these muffins yet. How many smartpoints are they?

    1. Trina @ Sally's Baking Addiction says:

      Hi Diane! We don’t usually include nutrition information as it can vary between different brands of the same ingredients. Plus, many recipes have ingredient substitutions or optional ingredients listed. However, there are many handy online calculators where you can plug in and customize your exact ingredients/brands. Readers have found this one especially helpful: https://recipes.sparkpeople.com/recipe-calculator.asp

  22. 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!

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