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Mini Pumpkin Muffins

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

  • 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

Keywords: The best whole wheat pumpkin muffins // healthy pumpkin chocolate chip muffins // mini pumpkin muffins healthy

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Mini Pumpkin Muffins


  1. Kelsie | the itsy-bitsy kitchen

    I still have Halloween candy lying around and I, clearly, don’t trick-or-treat. . .why does candy have to be so delicious? Anyway. LOVE these little cuties! Pumpkin muffins are one of my favorite things to bake in fall and winter!

  2. Mini muffins are just the perfect snack size! And love the inclusion of chocolate chips. We don’t have any candy left as the last few kids that came to the door got it all (I just dumped it in their bags!). But we have so many bags of chips and cheesies left. A salty snack is pretty hard for me to resist! So I’m definitely going to need some of these healthier muffins to balance things out! 😉

    • We’re all about the mini muffins here. My kids are 20 times more likely to eat a muffin when it’s mini sized, for whatever reason. Mini hands? You’re so smart to have just dumped your candy – we’re working through ours and now I just need it gone! I do love myself a salty snack though too!! Thanks friend! Have a great week!

  3. Why are mini foods just so much cuter than regular foods?!? Lol! Also, I absolutely loved that part where you said “I never forget” LOL! Same! If there is any type of sweet or candy in the house…I’m constantly thinking about it!!! These look so delicious and would make for a perfect Thanksgiving brunch!

    • They’re sooo much cuter, haha! I love all things mini too!! Hahah, Haylie. It’s so true. My husband laughs because he knows that I know exactly what’s in the pantry, and he has no idea….makes it easier to hide my sweets at least 😉 Thanks friend!

  4. I adore pumpkin and chocolate together! And the fact that these are mini just means that I can eat more, right? So much fun!

  5. Mini they may be, but I am sure that I can compensate in count what I (probably should) forego in volume:) Seriously, the fact that I have eight will not intimidate me at all:). Love that you can freeze them too – you never know when a craving may hit. Pinned.

  6. I just love mini food! Though, I’m bound to enjoy more than one, lol. Candy left? Nope, I gave every last bit of it away! Too much temptation. Though, I’m more of a sucker for cheezies 😉 And, no, I’m not giving all of those away…hehehe. These muffins look delicious, Katherine and love the option of making them mini or regular sized. Thanks a million for the shout out! XOXO

    • Soo good of you to give it away. I so wish I had done the same, because I can’t keep my hands off of it! I love cheezies too, and Cheetos. They’re a total guilty pleasure! Thanks Dawn! You’re welcome, hope you have a great week!!

  7. I never forget, either. That’s why I just threw all the leftover candy into a recipe for Scotcheroos. Because why not add insult to injury by combining a ton of sugary treats with chocolate chips, buttescotch chips, marshmallows and peanut butter? Good move. Ahem. Anyway these mini muffins look like a much healthier idea. Thanks for the balance, Katherine!

  8. I totally believe that these disappeared quick Katherine! They look just delicious. I can’t pass up anything pumpkin this time of year!

  9. These look so awesome! I’m obsessed with healthy yummy muffins and these are requesting my attention I feel! Pinning for later!! xo

  10. Mini muffins, I’m in! Look delicious, and no the chocolate chips are not optional 😉

  11. 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.

  12. 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!!

  13. These would disappear fast in my house too! Love that they’re mini, because that means I can have 2, right?

  14. 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.

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

  16. 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!!!

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