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. 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!!

  2. 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!!!!

  3. 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!

  4. Hi Sally do you think I could sub ghee for butter in this recipe without compromising the moistness?
    Thanks can’t wait to try!

  5. Hi Sally, over here in the UK ‘pumpkin puree’ is relatively hard to come by. Can I puree up a regular pumpkin? 

    1. You can absolutely make your own! Here’s a great tutorial.

  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.

    1. Glad they turned out with the extra pumpkin! And I always, always welcome more cinnamon in my baked goods. Thanks for reporting back!

  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. there’s no applesauce listed in ingredients. how much applesauce?

    1. There is no applesauce in this muffin recipe.

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

  12. Can I leave out the choc chips and bake them normal-size? for example 12 muffins?

    1. Yes, definitely. See my notes below the recipe for bake time/temperature.

      1. Ah! I see. thank you very much

  13. 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.

  14. James | Best Hoverboards 2016 says:

    These look perfect, and only 60 calories too. Definitely on our baking list for Fall. We love pumpkin!

  15. 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.

    1. A mini ice cream scoop is a great idea, thanks for sharing!

  16. Jared Rademaker says:

    I Tried Making These For My Health Class. I Changed The Recipe Too. I used only 1/3 a cup of brown sugar, 1/3 a cup of mini chocolate chips, and added 1/4 a teaspoon of turmeric. You Cant Even Taste They Turmeric and it makes it even more healthy.

  17. 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!

  18. 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.

  19. Sally, I’m trying desperately to get the recipe for pumpkin chocolate chip muffins but I can only find the picture and the comments/replies but now recipe. Could you help me?

    1. I had the same problem today. Made them the other day and they were so good we ate them all. Now I need to make more. Try this: http://www.delish.com/cooking/recipe-ideas/recipes/a43900/mini-pumpkin-chocolate-chip-muffins-recipe/

    2. Sorry about that! We had a coding error. Recipe’s back now!

  20. Can you please post the recipe for the whole wheat mini pumpkin muffins? I’ve had the tab open for a couple weeks to make them and was just about to start, when I discovered the recipe is no longer there! Thanks in advance.

    1. Sorry about that! We had a coding error. It’s back now!

      1. Thanks so much, Sally. I made them this morning and they are amazing! Wow. Thank you!

  21. 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. 

    1. 7!! Haha that is too funny. Thanks for sharing this with me! Thank you for the sweet comment, Emily. Happy you enjoy my blog– and dogs!

  22. can i use vegetable oil in place of butter/coconut oil?

    1. Vegetable oil would be OK.

  23. 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.

    1. I LOVE that you used raisins! So glad you liked them 🙂

  24. Do you know if these are ok for mailing? I didn’t want them to spoil or anything like that.

    1. Hannah Jackson says:

      I mailed them to a friend a few months ago and they did well.

      1. Perfect, thank you!

  25. 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!

  26. Hal Microutsicos says:

    Just baked these in a loaf pan with some white chocolate chips and raisins added, and melted coconut oil instead of butter. Cooked for ~27 minutes @ 350 then another 10 or so @325 to set. Worked out great!

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

    1. Absolutely

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

  29. 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.

    2. Coconut sugar

  30. 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.

    1. Hi Kim! So nice of you to ask– yes, you can just tell them the recipe is from my website! 🙂

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