Whole Wheat Mini 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!

I have a very serious question.

Do you think mini muffins are 100x better than regular size muffins?

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

Because they are. I mean, they’re so teeny tiny that you can eat 7 of them in one sitting. And that’s fine (dangerous?) because you still have a couple dozen left in the batch. And people aren’t really judging you for eating so many because they’re so cute and small. The muffins, not the people.

Hmm. Anyway. I shared these lil’ muffins on Delish.com recently. Have you seen them yet? Have you been obsessing over them like a mad woman? Just me? I love them. First of all, I made them with healthy eating habits on the mind. Not that eating 7 of them would be considered healthy, but stick with me here.

I use whole wheat flour in the muffins for healthy wholesome goodness. I also use unsweetened almond milk to keep the calories low. I don’t use a ton of sugar in the muffin batter– just enough to slightly sweeten the mini muffins. For flavor? Well, we’ve got the pumpkin puree. Shocker, right. Pumpkin spice, cinnamon, vanilla extract, and melted butter add even more flavor.

Don’t leave out that butter! A touch of melted butter helps make the muffins actually taste good. You know how healthier muffins sometimes taste… rubbery and dry? I shudder at the thought. They taste that way because there isn’t much fat in the muffin batter. So for today’s whole wheat pumpkin muffins, I use just enough butter to give the muffins a rich, tender texture but still keep them on the lighter side. Scrumptious.

Eggs! Also so important for moisture, tenderness, and a rich flavor. We’ll be using 2 in this whole wheat pumpkin muffin recipe. I recommend my go-to brand, Eggland’s Best; I use Eggland’s Best for any and all of the muffins I bake. Well, all of my baked goods really. And maybe scramble a few to enjoy alongside your pumpkin muffins. EB all the way.

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

I don’t typically post nutritional information for my recipes because my blog’s focus is having fun in the kitchen – not math. But, like these mini muffins, I was extra curious and I thought you would be too!

  • 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. Awesome by themselves and even better paired with hot coffee and a side of fruit & yogurt. You’ve got yourself a healthy breakfast (including CHOCOLATE!) that’s perfect for this time of year.

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

Are you having fun baking with pumpkin this fall? Here are all of my pumpkin recipes if you want more inspiration. And follow me on Instagram and tag #sallysbakingaddiction so I can see all the SBA recipes you make. And if you want to follow along on my book tour, find me on snapchat: sallysbakeblog. 


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. Sally;
     Hi,I decided that I am going to make the whole wheat mini pumpkin muffins recipe for the church when I sign up for the baking program so that there will be some delicious treats on Sunday mornings.
      What if somebody asks me for your recipe after they try the muffins?do I just tell the the staff that I got the recipe off of your website?
      I will also make the whole wheat mini pumpkin muffins for my family as well and I will let you know how we enjoy eating your muffins and how much the church staff and the rest of the congregation like and enjoy your muffins OK sally.

  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. 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!

  4. 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.

  5. 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!

  6. 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 🙂

  7. 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.

    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!

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I’m Sally, a cookbook author, photographer, and blogger. My goal is to give you the confidence and knowledge to cook and bake from scratch while providing quality recipes and plenty of pictures. Grab a cookie, take a seat, and have fun exploring! more about Sally