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The best mini pumpkin muffins with mini chocolate chips, whole wheat flour and loads of pumpkin pie spice! These healthy pumpkin chocolate chip muffins are a delicious bite sized breakfast or snack!

mini pumpkin muffins

Hi! How was Halloween? Do you have any candy left or were you one of those responsible parents that swapped it out for toys or donated it to the dentist or something like that!? We like candy ourselves too much so we still have a bunch kicking around. I am thinking I need to hide some of it or donate at least a bit, because it’s a bit out of hand. The kids have almost totally forgot about it….but I never forget….

So, these mini pumpkin muffins! I couldn’t let pumpkin season go by without posting one more pumpkin recipe! I’m pretty excited about this recipe. The kids literally ate the entire batch of them within 2 days. Maybe not even 2 days! They were a hit. 

My Mom makes some really great pumpkin chocolate chip muffins too, but I wanted to create my own from scratch using unrefined sugars (except for the chocolate chips) and a touch of whole wheat flour.  If you like my baby banana muffins, you’ll see that I took the same approach with half whole wheat and half all-purpose flour in the muffins. I find all whole wheat muffins don’t disappear quite as quickly around here as those made half and half!

How do you make mini pumpkin muffins?

I’m not even lying when I say you can whip these little gems up in a heartbeat! I always start with my dry ingredients, followed by the wet, then mix them together JUST until there are no flour streaks left.

Fill your muffin tin 3/4 full, using a small cookie scoop. This recipe makes exactly 24 mini muffins! You can use cupcake liners or just spray your muffin tin with non-stick spray.

Do you have to use half whole wheat flour?

You can absolutely substitute for either all whole wheat, or all white flour. No other recipe adjustments would need to be made, but if using all whole wheat, you may have to add a touch more almond milk to the batter if it’s looking a little stiff. 

Another substitution you may want to make is switching out the maple syrup for something else. You can do a 1-1 switch with honey, or brown sugar. 

Bake the muffins for 10-12 minutes. Check them after 10 minutes with a toothpick, and if it comes out clean then they’re good to go! If there’s a bit of batter on the toothpick, bake the muffins for an additional 2 minutes before checking again.

mini pumpkin muffins

The mini chocolate chips are also completely optional, but they are pretty darn delicious in the muffin!! And not that your kids need any more encouragement to eat a delicious little muffin, the mini chocolate chips will definitely have them begging for more!

Can you make these mini muffins in a regular sized tin?

Yes! You can keep the recipe the same, and use a 12-count muffin tin instead. Fill the regular muffin tin to 3/4 full and bake for 18-20 minutes! You could use regular sized chocolate chips for the regular sized muffins too.


mini pumpkin muffins

mini pumpkin muffins

We love mini muffins – if you do too you will love these other recipes from the blog!

Oh – and if you need a quick DIY pumpkin pie spice for the muffins, this is a great recipe from my friend Dawn!

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mini pumpkin muffins

Mini Pumpkin Muffins

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5 from 14 reviews

  • Author: Katherine | Love In My Oven
  • Total Time: 25 minutes
  • Yield: 24 mini muffins 1x


The best mini pumpkin muffins with mini chocolate chips, whole wheat flour and loads of pumpkin pie spice! These healthy pumpkin chocolate chip muffins are a delicious bite sized breakfast or snack!


  • 1/2 cup whole wheat flour
  • 1/2 cup all-purpose flour
  • 1 tsp baking powder
  • 1 tsp baking soda
  • 1/4 tsp salt
  • 1 tsp pumpkin pie spice*
  • 1 tbsp cinnamon
  • 1/4 cup oil (grapeseed, avocado)
  • 1 large egg
  • 1/3 cup maple syrup
  • 1 cup pumpkin puree
  • 2 tbsp unsweetened almond milk
  • 1 tsp pure vanilla extract
  • 1/3 cup mini chocolate chips


  1. Preheat the oven to 350F and line a 24-count mini muffin tin with paper liners, or spray the cavities well with non-stick spray.
  2. In a large bowl, sift together both flours, the baking powder, baking soda, salt, pumpkin pie spice and cinnamon. Set aside.
  3. In a medium sized mixing bowl, whisk together the oil with the egg and maple syrup. Add the pumpkin puree, almond milk and vanilla extract and whisk well. Pour the wet ingredients into the dry, and stir just until there are no remaining streaks of flour. Add in the mini chocolate chips, stirring gently with a wooden spoon to incorporate.
  4. Using a small cookie scoop or spoon, fill the muffin cavities 3/4 cup full and bake for 10-11 minutes. Check after 10 minutes, and using a toothpick, insert into the center of the muffin and if there is batter remaining on the toothpick, bake the muffins for another minute or two. If it comes out clean, the muffins are done! Remove the muffins to a wire rack to cool completely.

Leftover muffins can be kept at room temperature, in an airtight container for 2-3 days, in the fridge for 4-5 days or in the freezer for up to 2 months.


*If you don’t have pumpkin pie spice, substitute with 1/4 tsp ground ginger, 1/4 tsp cinnamon, 1/4 tsp all-spice, 1/4 tsp nutmeg.

**For regular sized muffins, use a 12-count regular sized muffin tin and bake for 18-20 minutes.

  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Category: breakfast
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Mini Pumpkin Muffins

About Katherine

Heeey! Thank you for stopping by! I like 30-minute dinners and giant peanut butter cups made with only 3 ingredients. I LOVE food! If you do too, you're in the right place.

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  1. Mini muffins are the BEST! Perfect for a bite-sized snack or for kids’ lunches. And who doesn’t love a pumpkin muffin with CHOCOLATE?! Pinned.

  2. I can’t forget about the candy either!! My husband is so good at saving treats for later, but those mini candy bars never stop calling my name 😉 These pumpkin muffins look incredibly delicious Katherine, and I love the healthy ingredients, beautiful recipe!!

    1. Haha, I’m glad I’m not the only one. If they’re in the house I’m thinking about them!!! Thanks Catherine!

  3. Our neighborhood didn’t trick or treat this year. Thank god! These muffins sound delish! Mini cupcakes don’t stick around long in my fridge so maybe I should freeze some of these hehe.

    1. Haha, so funny Ros. We love trick or treating! I might feel differently when my kiddos grow up though. You should make a double batch and freeze half!!

  4. Yes!! I want two or three of these mini muffins for breakfast. And as always I appreciate you making these healthier!! Yum!

    1. Definitely need at least 3, Kelly!! Thanks pal! I love making things delicious without all the junk 🙂

  5. These look like a great snack! I have bigger kids, so I think I’ll make the regular size. I have bunch of pumpkin in the freezer that I’m dying to use!!!