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: 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. 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. 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! 

  2. 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! 

  3. Just threw the second batch in the oven!! We love these – and really every recipe on your site!! I would love to see more whole wheat recipes and maybe some without sugar but honey or maple syrup as a sweetener? Food for thought – thanks for another great breakfast!!

  4. Welp….I think your recipe has dethroned my long-reigning KAF one as THE KEEPER!!!  These were just fabulous!  And soooo easy!  I rarely do minis and always use paper cups with the regulars, RUTROW on me for forgetting to spray the pan!  Half stuck a bit on the bottom edges–but that means half came out intact!! 🙂 I either need to invest in mini paper cups or find that baking spray!  Seriously, folks–MAKE THESE!!!!

  5. I made these muffins but decided to make them the standard size (since mini muffins trick my brain into thinking that 5 at a time are a good idea lol).   They turned out nice and tall, moist and not too sweet.  Some pecans might have *accidentally* fell into the mix. 😉
    Great muffins! It’s so nice to have whole wheat muffins that aren’t dry or dripping with oil! Thank you Sally!

  6. Hi Sally, I made these last night and they are truly lovely – not dry at all and spicy flavor.  I topped mine with some chopped pecans and pumpkin seeds.  I am wondering how this “healthy cake” would turn out baked in a half cookie sheet/pan topped with a light layer of cream cheese frosting and chopped nuts or something?  Any thoughts?  Thank you in advance Sally.

    1. I think this would be a great recipe to double and bake in an 11×7 or maybe a 9×13 pan. Unsure of the bake times though!

  7. I just made these using butternut squash.  They are delicious! 
    Thank you,  Sally

  8. These are amazing!! I have tried a few of your other muffin recipes, and loved them so much I just keep coming back for creative ways to get more vitamins with less sugar into my two growing toddlers 🙂 I used (completely by accident) an entire can of pumpkin instead of just the 1 cup…and they turned out beautifully. Not overly dense, they rose well, and the flavor still seemed to be pretty well balanced (I did increase the cinnamon though…my boys LOVE their cinnamon in EVERYTHING). Thanks for another great treat that was fun and easy to make, that used items I already had laying around my kitchen.

  9. These muffins came out tasting delicious, thank you for creating this recipe, but whenever I use whole wheat flour the tops come out sort of dry and uneven and not as attractive looking as the muffins in your picture. Could it be the type of flour I am using (Gold Medal whole wheat), or something else I am doing? Any ideas? Thanks again.

  10. I made these for my son. I left out the choc chips but they were still so delicious! Yummo!

  11. I made these yesterday. They are delicious!
    They didn’t come out orange like yours, though. I made my own pumpkin puree. I don`t know if that could have made a difference.

  12. Just made these yesterday – I had some canned pumpkin in the freezer – and they turned out terrific & tasty!!! Used 1 cup whole wheat and 1 cup all purpose flour. I used a mini ice-cream scoop that made scooping out the batter into the mini muffin tin much more easier.

  13. Loved this recipe. Perfect balance of sweetness, and the spices were spot on. I made full size muffins. Flavorful. Moist. Perfect instructions. One can tone down the WW flour by substituting flours of his/her choice. Also using dried fruits (cran, cherry, raisins, currants, etc) instead of chips. Or substituting different baking chips. Lots of variations. Danka!

  14. Love Love Love these muffins! I make them regular sized, with walnuts, butterscotch chips, etc. They are so tasty every time! Just popped a batch in the oven.

  15. These muffins are so delicious and moist, which you don’t always get in an entirely whole wheat flour only baked good. I made them for a friend to take to work for the week as a healthy breakfast option. (I did omit the chocolate chips as he’s not a chocolate fan, but determined they were still delicious when I taste tested one.) When I dropped them off at his place, his reaction was that there were way too many and he would try his best to eat them all. Well the next morning I got a text letting me know that the muffins were so good, he had eaten somewhere in the ballpark of 7 of them! No need to worry about whether or not they’ll get eaten, I guess. 🙂 Anyway, all that to say, this recipe is a huge winner and I plan to make these again for sure. Love your blog, Sally, (and your adorable dogs!), and am looking forward to making more of the recipes. 

  16. I substituted raisins for the chocolate chips, These muffins were DELICIOUS! They were not grainy at all, like most of the whole wheat muffins that I make are.

  17. Hannah Jackson says:

    I make these muffins again and again; they’re one of my favorites! I’ve been really reluctant to use regular chocolate chips but today I had no choice, but they still worked really well. So if you’ve only got regular size give it a go anyway!

  18. Could I use all-purpose flour in place of whole wheat flour?

    1. Absolutely

  19. Made these this morning and they came out great. Thanks, Sally! I’m really enjoying your wholemeal recipes. Keep ’em coming!

  20. What can I use instead of brown sugar? Can I use agave or honey? How much should I use?

    1. I don’t suggest swapping in a liquid sweetener.

  21. 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. 

  22. 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!

  23. 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.

  24. 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!

  25. 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 🙂

  26. 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.

  27. 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!

  28. 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!

  29. 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.

  30. 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.

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