Pumpkin Spice Muffins Recipe

These cute, pumpkin spice mini muffins are perfectly portioned for a sweet treat!

So if you know anything about me, you know that I love a good muffin. And I’m here to tell you that the apple does NOT fall far from the tree. Mini chef loves them just as much. Maybe more! But lately, I’ve noticed that if I give him a whole muffin, he’ll eat the entire thing and want more. So to remedy that, I started baking mini muffins on a more regular basis.

One from a big batch of Pumpkin Spice Mini Muffins sits on a white plate in front of a pumpkin.

So far, it’s working out pretty well. I can give him a few and he feels like he got more than one without actually going overboard. It’s a win-win in my motherhood book.

The insides remain soft and pumpkiny which we love, and the pumpkin spice is definitely there without being overpowering.

Hope you enjoy these as much as we have!

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Clean Eating Pumpkin Spice Mini Muffins Recipe

Pumpkin Spice Muffins

Note: making larger muffins is not recommended. This batter works far better when made as mini muffins.
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Course: Breakfast, Dessert, Snack
Cuisine: American
Prep Time: 15 minutes
Cook Time: 40 minutes
Total Time: 55 minutes
Servings: 30 mini muffins (approximate)
Calories: 57kcal


  • Mini muffin pan


  • 2 cups whole wheat pastry flour (affiliate link)
  • 1 tbsp. baking powder
  • 2 tsp. pumpkin pie spice (no sugar added)
  • 2 large egg whites
  • cup honey
  • ¾ cup unsweetened apple sauced
  • 2 tbsp. oil (I used safflower)
  • ¼ cup unsweetened almond milk
  • 15 oz. can pumpkin puree (not pumpkin pie filling)


  • In a large bowl, whisk together the flour, baking powder and pumpkin spice.
  • In a separate bowl, combine the remaining ingredients and whisk to combine.
  • Combine the liquid into the flour and stir until smooth.
  • Spoon into mini muffin tins (I used non-stick with a light spray of olive oil).
  • Bake at 350 degrees F. for 40-50 minutes.
  • Allow to cool and enjoy!


Please note that the nutrition data below is a ballpark figure. Exact data is not possible.


Serving: 1muffin | Calories: 57kcal | Carbohydrates: 11g | Protein: 1g | Fat: 1g | Sodium: 8mg | Potassium: 120mg | Fiber: 1g | Sugar: 4g | Vitamin A: 2210IU | Vitamin C: 0.7mg | Calcium: 32mg | Iron: 0.6mg

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  1. graciouspantry says:

    I don’t know if it’s clean, but I’m sure it would substitute just fine.

  2. Pingback: Clean Eating Recipes | 19 Clean Eating Pumpkin Recipes
  3. graciouspantry says:

    Yes, you can sub with milk. Any oil will work really, you just have to watch the flavor it imparts. You could try grape seed oil or extra virgin olive oil. Even avocado oil might work.

  4. I need to replace the WWPF with brown rice flour…can you give me the measurements to make equivalent please. My BRF mixture has something to replace the gluten in WWPF.

    1. graciouspantry says:

      Boy, that’s a tough one. As long as you are replacing the gluten with something, I would imagine that you could sub with nearly equal amounts. Just a guess though because I’ve never actually done it. Sorry, wish I could be more help.

  5. Pingback: Clean Eating Recipes | Clean Eating Foods That Travel Well
  6. I tried these out last night, they tasted great, but stuck to my mini muffin pan. I used olive oil to spray the cups and they stuck and burned a bit on the outside. I then tried liners for the second batch and they got stuck to the paper. I’m not sure why I’m having trouble with them!

    1. graciouspantry says:

      Hmmm… have you tried the foil liners yet? They seem to work best in that department. Also, be sure you let the muffins cool fully before removing. That always seems to help me.

  7. I’ve made these mini muffins twice now and they have not come out right either time. The first time I thought it may have been the pumpin I used (canned from trader joes) so the next batch I tried canned pumpkin from whole foods. Both batches were burnt on the tops and gooey in the middle. I am determined to get this right. Maybe I need to reduce the temp?

    1. The Gracious Pantry says:

      Candace – It could certainly be the oven, but did you make any other changes? Perhaps to the flour?

  8. Nope, I followed the recipe exactly with whole wheat pastry flour, etc. I had leftover batter and made a few extra with putting them in the oven at 320 for 50 minutes and they were still gooey 🙁 I haven’t had issues with any other mini muffins, just the ones that require pumpkin.

    1. The Gracious Pantry says:

      Candace – Odd. Is your oven actually baking at the temp it says it is? Do you have an oven thermometer that sits inside it to verify the temp? If you try them again, back off a bit with the apple sauce. Try maybe 1/4 – 1/2 cup instead of 3/4. Also, are you at a higher altitude?

  9. I do have an oven thermometer and have verified the temp. I live in Georgia so no altitude issues. I may try a third time and reduce the applesauce like you said..third times a charm right? 🙂

    1. The Gracious Pantry says:

      Candace – Yup!! Let me know how they turn out!

  10. I love your recipes! I only came across your site a week ago but have already made several things and they’ve all been so yummy. Unfortunately these muffins didn’t really turn out for me. They tasted great but were undercooked inside and overdone on the outside. I didn’t change anything and I used a mini muffin tin. I’m going to try your suggestion of lowering the temp and baking longer next time to see if that helps.

    1. The Gracious Pantry says:

      Tanya – Sorry to hear that! I also recommend buying a stand-alone thermometer for the inside of your oven to be sure it’s baking at the temp that it says it is. Sometimes the temp on the oven and the temp IN the oven are two very different things. They are pretty cheap, usually between $5 and $8. Let me know how they turn out if you try them again!

  11. Where can I purchase Whole Wheat Pastry Flour, and how is it different from whole wheat flour? My grocer doesn’t carry it, and I wasn’t able to find it at Trader Joes.

    Thank you,

  12. I can’t wait to get back from my trip to make these!

    1. The Gracious Pantry says:

      Monica – I hope you enjoy them!

  13. Is it supposed to be gooey in the middle like what the pumpkin looked like in the can or like a muffin? If so…i left it in the oven hoping it’ll bake in the middle and ruined an entire batch! Maybe pictures of what the inside look like will help.

    1. The Gracious Pantry says:

      Deidra – It shouldn’t be THAT wet in the middle. A little moist maybe, but not wet like what came out of the can. If you try it again, I would cover the muffins (when the tops have solidified) with a lose sheet of aluminum foil so you can bake longer without burning them. It’s most likely just a difference in our ovens. These were the mini muffins you did, right? Because if you made bigger ones, they will not fully bake.

  14. Found this recipe on pinterest, the muffins just came out of the oven. I only used about 1/4 cup of honey, and was even able to make around 45 mini muffins! Can’t wait to taste them, thanks!

    1. The Gracious Pantry says:

      Gracie – My pleasure! I hope you enjoy them!