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Home » Recipes » Healthy Muffin Recipes

Pumpkin Chocolate Chip Mini Muffins

By: Kathryn Doherty | Last Updated: Mar 5, 2025 | Published: Oct 1, 2015
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These addictive pumpkin chocolate chip mini muffins are 100% whole wheat and naturally sweetened with no oil or butter needed. They are great for a delicious, healthy snack!

Five mini pumpkin chocolate chip muffins on a small black plate with more mini muffins and some fall decor nearby.


 

Hello October!

I think it may be my most favorite month. It’s got pumpkins, it’s got beautiful leaves, it’s got my birthday near the end of the month! And, of course, Halloween.

We start gearing up for the season at the end of September and I’m always so ready for it to be today. October 1st!

I can finally put out pumpkins on the front steps and decorate the house with leaves and gourds and maybe a spooky skeleton or two.

It’s kinda my holiday.

Also, October means I can continue to eat ALL the pumpkin things. All day long. All month long. And well after that...

Like these insanely addictive, amazingly pop-able pumpkin chocolate chip mini muffins. I find myself reaching for one at pretty much all hours of the day.

They are so soft and sweet and perfectly chocolatey!

A black plate with a mound of mini chocolate chip pumpkin muffins with fall leaf decor in the background.

And why not?

They’re completely whole wheat, have pumpkin and applesauce and are naturally sweetened with honey. No oil or butter here at all.

(Y'all know I have some muffin munckins. You can check out all of my healthy muffin recipes here.)

And less than 70 calories per mini muffin!

So yes, I think I will have another. And another. And… You’ll need to look away so I don’t embarrass myself.

OK, let's get to baking.

Mini pumpkin chocolate chip muffins on a small black plate with faux fall leaves and pumpkin decor nearby.

I’ve got some notes and tips coming up below on how to make pumpkin chocolate chip mini muffins. Just tryin’ to be helpful.

If you want to jump on down to the recipe, simply scroll right on through the rest of the text. The recipe card is near the bottom of the page, above the comments section.

Recipe Notes:

  • Flour: I use white whole wheat flour in my baking, but whole wheat flour or regular all-purpose flour would work here as well.
  • Honey: I use honey as the sweetener but I think maple syrup would be fine here too. And if you need these to be vegan, you can also use a flax egg as a substitute for the egg.
  • Pumpkin: Make sure you use pumpkin puree, NOT pumpkin pie filling.
  • Yield: The recipe makes about 30 mini muffins. You can also make 24 mini muffins and end up with enough batter for about 3 large muffins. Those need to bake for about 20 minutes.

Also, I wanted to share some storage tips for this muffins.

The extras will keep for about 5 days at room temperature, in a sealed ziptop bag or plastic container.

You can also freeze the leftovers! Once cooled, pop the extras in a ziptop plastic freezer bag -- that's labelled -- and will keep in the freezer for up to 5 months.

You can either thaw them in the fridge overnight or just pop them straight from freezer to microwave to quickly warm them up.

A plate full of mini muffins with some fall leaf decor in the background.

Pumpkin + chocolate + itty bitty muffins. Yes please.

I sure am glad to see you again, October. So are my two little kiddos, who also devour these and wanted more, more more. Can't blame ya, kids!

And if you're looking for other fun fall treats, try my pumpkin baked oatmeal with chocolate chips, chocolate pumpkin granola and chocolate chip apple cake.

Also, check out ALL of my healthy fall baking recipes here. ❤️

Welcome October with me and bake up a batch of these crazy good mini muffins.

Enjoy!

XO,

Kathryn

Mini pumpkin chocolate chip muffins on a small black plate with faux fall leaves and pumpkin decor nearby.
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4.50 from 2 votes

Pumpkin Chocolate Chip Mini Muffins

These addictive pumpkin chocolate chip mini muffins are 100% whole wheat and naturally sweetened with no oil or butter needed. They are great for a delicious, healthy snack!
Prep Time15 minutes mins
Cook Time10 minutes mins
Total Time25 minutes mins
Yield: 30 mini muffins

Ingredients

  • 2 cups whole wheat flour (see notes)
  • 1 teaspoon baking soda
  • ¼ teaspoon salt
  • 1 teaspoon cinnamon
  • 1 large egg
  • 1 cup pure pumpkin puree (not pumpkin pie filling)
  • ½ cup unsweetened applesauce
  • ⅓ cup honey
  • 2 teaspoons vanilla extract
  • ¾ cup mini chocolate chips

Instructions

  • Preaheat oven to 350. Spray mini muffin pans with cooking spray.
  • In a large bowl, combine the flour, baking soda, salt and cinnamon. Mix well.
  • In a separate, small bowl, combine the egg, pumpkin puree, applesauce, honey and vanilla. Mix very well.
  • Add the wet ingredients to the dry ingredients and stir just to combine. Stir in the mini chocolate chips.
  • Divide the batter between the mini muffin pans. Fill each muffin cup to the very top.
  • Bake at 350 for 10-13 minutes, until done.

Notes

Flour: I use white whole wheat flour for my baking. However, you could also substitute regular all-purpose flour for this recipe or use a combination of the two.
Honey: I use honey as the sweetener but I think maple syrup would be fine here too. And if you need these to be vegan, you can also use a flax egg as a substitute for the egg.
Yield: You can also make 24 mini muffins and end up with enough batter for about 3 large muffins. Those need to bake for 20 minutes.
Storage: The extras will keep for about 5 days at room temperature, in a sealed ziptop bag or plastic container.
You can also freeze the leftovers! Once cooled, pop the extras in a ziptop plastic freezer bag -- that's labelled -- and will keep in the freezer for up to 5 months. You can either thaw them in the fridge overnight or just pop them straight from freezer to microwave to quickly warm them up.

Video

Nutrition

Serving: 1mini muffin | Calories: 67kcal | Carbohydrates: 13g | Protein: 2g | Fat: 2g | Saturated Fat: 1g | Polyunsaturated Fat: 1g | Cholesterol: 6mg | Sodium: 63mg | Fiber: 1g | Sugar: 6g
Tried this recipe?Leave a comment below or follow me on Instagram @familyfoodonthetable and tag me in your photo!
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Reader Interactions

Comments

  1. Amanda | The Chunky Chef

    October 01, 2015 at 9:09 pm

    I love mini muffins! These look so perfect for Fall!

    Reply
    • Kathryn

      October 02, 2015 at 9:10 am

      Me too - mini means I can eat more 🙂

      Reply
  2. the lovely kitchen

    October 02, 2015 at 7:58 pm

    These look delicious - and so kid friendly! I bet they don't even notice they're somewhat healthy 🙂 I'll have to test them on my daughter.

    Reply
    • Kathryn

      October 04, 2015 at 1:53 pm

      They are very kid-friendly. Very mama-friendly too 😉 My favorite kind of treat... Hope you both love them!

      Reply
  3. Sarah James @ Tales From The Kitchen Shed

    October 05, 2015 at 11:49 am

    They look delicious & even better that they're naturally sweetened too, yum 🙂

    Reply
    • Kathryn

      October 05, 2015 at 4:09 pm

      Thanks Sarah! They are a lovely wholesome little snack 🙂

      Reply
  4. Alli @ Tornadough Alli

    October 18, 2015 at 7:38 pm

    I love myself a good muffin! These look so flavorful and I'm a pumpkin addict so they will need to be made this fall for sure. Thank you for sharing with us at #ThrowbackThursday link party! Hope to see you again this week!

    Reply
    • Kathryn

      October 19, 2015 at 3:18 pm

      Me too Alli! Muffins are the best, as is pumpkin. And if there's chocolate chips in the muffin, all the better 😉 Thanks for hosting a great party! XO

      Reply
  5. Hailey Maloney

    October 30, 2016 at 11:13 pm

    Loved the flavor on these but they turned out really dry and dense for me...even after I added a touch of water to the batter. Maybe next time I need to spoon the flour into the measuring cup instead?

    Reply
    • Kathryn

      October 31, 2016 at 7:56 am

      Hi Hailey, yes, measuring the flour by spoon should help. The density can also depend on your pumpkin puree. Some cans/brands are really dense and thick and others are much more liquidy. If your pumpkin puree seems thick, you may want to add an extra 1/4 cup applesauce or water to thin it out. Hope that helps!

      Reply
  6. Garfield Hiscock

    October 19, 2017 at 9:59 am

    I made regular muffins and used 1/4 c each of milk chocolate, semi-sweet chocolate and butterscotch chips. They were a-mazing!

    Reply
    • Kathryn

      October 19, 2017 at 2:26 pm

      I'm so happy to hear you loved the Garfield! I love your substitution of the trip of chips - yum!

      Reply
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Meet Kathryn

Hi there! I’m Kathryn Doherty, a cookbook author, mom of two, and devoted food and home cooking nut. I’ve got lots of easy recipes to help you get delicious food on the table for your family!

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