Pumpkin Spice Muffins Recipe

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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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Pumpkin Spice Muffins Recipe Card

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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
Author: The Gracious Pantry


  • 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
  • β…“ cup honey
  • ΒΎ cup unsweetened apple sauced
  • 2 tbsp. oil (I used safflower)
  • ΒΌ 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. Pumpkin makes me feel all warm and cozy and “fallish”. These sound delicious! I think the idea of mini-muffins makes you feel like you are eating more without actually doing it. Great trick on our minds!

    1. Anonymous says:

      Marisha – Exactly!!

  2. Stephanie Gibbs says:

    Just found your site and ready to try some things. I couldn’t find whole wheat pastry flour but did find white whole wheat flour. Will that work?

    1. Anonymous says:

      Stephanie – Yes, that should work. Welcome and enjoy!

  3. I crave everything pumpkin! so excited for this recipe! you’re awesome!

    1. Anonymous says:

      Steph – Thank you! I hope you enjoy them!

  4. what do you recommend as a substitute for almond milk – my son is allergice to tree nuts


    1. Anonymous says:

      Erin – You can use regular milk too. 1% works well.

  5. Health Freak College Girl says:

    i love pumpkin so i definitely need to try these out πŸ™‚

    1. Anonymous says:

      HFCG – I hope you enjoy them!

  6. Superfood Sisters says:

    Love anything pumpkin this time of year!! I am always looking for breads and muffins that don’t add a ton of sugar. Can’t wait to try these!!

    1. Anonymous says:

      SS – Wonderful! I hope you enjoy them!

  7. Anonymous says:

    Jodi – I don’t recommend this batter for larger muffins. It won’t cook correctly. I’ll see if I can develop a different recipe for larger muffins.

  8. Anonymous says:

    Kelly – Fabulous! I hope you enjoy them!

    1. Kelly @ City Mom says:

      I did!! I replaced the whole wheat flour with brown rice flour as I am not a gluten consumer. I find when I bake with alternative flours they product always comes out a little dense, but they are still very delicious!

      1. Anonymous says:

        Kelly – Fantastic!! Glad it worked out!

  9. Anonymous says:

    Kimberly – Thanks and enjoy!

  10. My little man LOVES mini muffins! It used to be the only way I could get veggies into him. I’d make zucchini, carrot muffins and he would gobble them up, thinking they were a treat. Thanks for another wonderful recipe!

    1. Anonymous says:

      Irene – You’re welcome! I hope the munchkin likes them!

  11. I just like muffins. All kinds (gluten-free) and all sizes. Definitely have to try these.

    1. Anonymous says:

      Jenni – I’m with you on that. Muffins are wonderful!

  12. Clarisse Miller says:

    oh wow these are moist! I’m trying them for the first time in my babycakes mini muffin maker and I’m having to keep them in significantly longer than the banana muffins Tiff has on this site. I over filled the tins because I underestimated the cooking time so they are burning on the outside and too soft in the middle! oh well next batch i’ll make really mini teeny tiny muffins!

    1. Anonymous says:

      Clarisse – Ya, I’m not sure about that mini muffin maker either. You might try a batch in the over to see if there’s a difference.

  13. Clarisse Miller says:

    First comment from 2 year old was “THIS IS GOOD! and yummy!” I thought I’d want more sweetness but i’ve been eating a lot of refined sugar lately, so I’ll go with the toddler’s opinion!

    1. Anonymous says:

      Clarisse – Wonderful! And yes, if you’ve had a lot of sugar lately, they won’t taste all that sweet to you. Glad the munchkin liked them though!

  14. Anonymous says:

    Brandy – That’s wonderful!

  15. Anonymous says:

    Anon – You may need to reduce the temp to about 325 and bake for much longer to get the centers cooked all the way. Gook luck, and let me know how they turn out!

    1. Anonymous says:

      Oh the humanity! They totally didn’t come out. They were getting burned on top and not done in the middle. I’ll have to get me a mini-muffin tin and try them again. We settled for cereal this morning instead. πŸ™

      1. Anonymous says:

        Anon – Oooooh noooooo!!! I’m so sorry. I’m sure they will be yummy with the mini muffin tins though. Boo hoo!

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  17. Anonymous says:

    Any light tasting oil will work.

  18. graciouspantry says:

    Felps – Never thought to try that!

  19. Charlie Auger Mace says:

    Do they really take 40 – 50 minutes to cook? Excited to see how mine turn out!

    1. graciouspantry says:

      Every oven is different, but for me, that’s how long they took.

      1. Charlie Auger Mace says:

        I have a feeling that my mini muffin pan is smaller than an american one! They turned out great! Cooked in about 15mins. I made them to go with a clean pumpkin oatmeal smoothie, for brunch tomorrow with my friend who is new to eating clean! Thanks again for putting in all the hard work to make all of us look good πŸ˜‰ I tell everyone I know about this fab blog!

        1. graciouspantry says:

          Awesome! Thank you so much!

  20. graciouspantry says:

    I’d have to see the recipe.

  21. graciouspantry says:

    Sorry, all fixed.

  22. graciouspantry says:

    you can try it, but I think you need the gluten on these. Sorry.

  23. Sorry, just to clarify, by mini muffins do you mean baking them in a small cupcake tin?

    1. graciouspantry says:

      Yes, there are mini muffin tins you can buy.

  24. LeighStella says:

    Mine only took about 15 minutes in my tiny little muffin pan…so good, especially with a little drizzle of honey. Best not to wake little ones up from their nap to taste them, but so excited to serve these clean, yummy treats to my kiddos! Thanks!

    1. graciouspantry says:

      Haha!!! No, we wouldn’t want to wake them….
      Glad you enjoyed them!

  25. graciouspantry says:

    Any mild flavored oil you like.

  26. graciouspantry says:

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

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  28. 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.

  29. 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.

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  31. 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.

  32. 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?

  33. 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 πŸ™ 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?

  34. 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? πŸ™‚

    1. The Gracious Pantry says:

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

  35. 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!

  36. 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,

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

    1. The Gracious Pantry says:

      Monica – I hope you enjoy them!

  38. 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.

  39. 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!

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