17 Best Healthy Pumpkin Muffins

~ After spending hours upon hours sorting through pumpkin muffin recipes, these 17 standouts absolutely rose to the top as the very best healthy pumpkin muffins I found. Whether you’re looking for lots of whole grain goodness, or maybe you need paleo recipes or ideas that are gluten free … trust me, there are plenty of ideas here that’ll inspire you to fire up that oven! ~

From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

As soon as fall rolls around, it seems like everybody can think of just one thing: pumpkin! From Starbucks’ PSLs to pumpkin muffins and pumpkin pie, the foodie buzz is all about pumpkin.

And yeah, we’ve got pumpkin recipes here at THK. Of course! An easy hummus, a quick vegetarian chili, a super-fast pumpkin pie oatmeal. And of course … our own pumpkin muffins! The recipe we’ve loved for years and years, the one that’s nicknamed “Kids’ Favorite.” The one that everybody always asks for the recipe. Our beloved Healthy Pumpkin-Chocolate Chip Muffins (peek down below … they’re #1 on my list!).

But I wanted more. More, MORE, MORE pumpkin muffin ideas. More than I could think up all by myself. (And I figured you just might want more, too.)

So I did what I always do in these situations. I asked my food blogger compatriots to share their healthy pumpkin muffin recipes.

And I’ve gotta tell ya. They kind of blew me away. Not only were there flavor combos I’d never imagined, and healthification tricks I can’t wait to try … I also learned so much about specialized baking techniques for diets like paleo and gluten free. Although we have lots of recipes here on our site that just happen to be paleo or gluten free, I don’t specifically focus on either, so the techniques for pulling off the specific alchemy of those kinds of baked goods was something I knew almost nothing about.

Until now!

There are some crazy-cool strategies in here that I can’t wait to try, not because we follow a specific diet, but because they just sound fabulously delicious (and are really nutritious, too)!

Trust me. Whether you’re looking for healthy pumpkin muffins that define “healthy” as:

  • Whole grain
  • Low fat
  • Refined sugar free
  • Paleo
  • Gluten free
  • Dairy free

… there are plenty of ideas here to inspire you!

And, if you’re like me, and you just enjoy trying new flavor combinations and new baking techniques, honing your baking skills by attempting something entirely different … well, this collection of recipes has ya covered there, too!

Drool your way through this list, and then tell me … which one are you making first?!?

From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Healthy Pumpkin-Chocolate Chip Muffins (with optional Caramel Swirl) from Two Healthy Kitchens

This is our go-to pumpkin muffin recipe here at THK. Wonderfully decadent, with bursts of creamy chocolate and {optional} swirls of date-infused caramel filling! No doubt – these are definitely called “Kids’ Favorite Muffins” for a reason! Try these for grab-and-go breakfasts with the easy make-ahead and freezing tips, or bake ’em up as darling “mini” muffins for quick snacks!

Whole Wheat    Low Fat

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Pumpkin Sticky Bun Muffins from Lexi at Lexi’s Clean Kitchen

Lexi describes this pumpkin muffin recipe by saying, “Pumpkin + cinnamon bun filling + ooey gooey glaze = some serious muffin perfection.” Seriously … what more could you need in a muffin?!?!

Gluten Free    Paleo    Dairy Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Paleo Pumpkin Muffins from Rachel at Bakerita

These paleo muffins are made with coconut flour and almond butter. They’re lightly spiced, and topped with an alluring mix of cinnamon, coconut sugar, and a sprinkle of pepitas.

Gluten Free    Paleo    Dairy Free    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Coconut Flour Pumpkin Banana Muffins from Stephanie at Apples for CJ

What a fun idea – sort of a mash-up of pumpkin muffins meet banana bread! Plus classic fall flavors from pumpkin pie spices and maple syrup – yum!

Gluten Free    Paleo    Dairy Free    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Paleo Pumpkin Muffins from Chrystal at Gluten-Free Palate

With just 10 minutes of prep time, these beauties will be ready for noshing in no time flat!

Gluten Free    Paleo    Dairy Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Pumpkin Cheesecake Muffins from Natalie at Natalie’s Happy Health

Decadent enough for dessert, these pretty muffins are filled with warm, pumpkin pie spices and topped with irresistible cheesecake swirls!

Whole Wheat    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Cranberry Pumpkin Muffins from Karman at The Nutrition Adventure

Brimming with TWO holiday flavors … pumpkin plus fresh, juicy cranberries! Absolutely perfect for Thanksgiving!

Whole Wheat    Low Fat

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Pumpkin Apple Muffins from Katja at Savory Lotus

These just scream Autumn! Cinnamon-y goodness, studded throughout with juicy chunks of fall apples … plus a sweet apple topping, too!

Gluten Free    Paleo    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Paleo Pumpkin Muffins with Streusel from Erin at Texanerin Baking

Oh my goodness … that crumbly pecan streusel topping! What a gorgeous (and delicious) touch!

Gluten Free    Paleo    Dairy Free    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Maple-Sweetened Pumpkin Oatmeal Muffins from Aysegul at Foolproof Living

Whole wheat and ground oats equal lots of whole-grain goodness, and a touch of maple syrup adds natural sweetness. Toss some pumpkin seeds and extra oats on top for a pretty finishing touch!

Whole Wheat    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Paleo Pumpkin Zucchini Muffins from Laura at Joy Food Sunshine

Packed with both zucchini and pumpkin, there’s a whole lotta veggie goodness going on here. (So you can definitely feel ok about throwing in a few decadent chocolate chips!)

Gluten Free    Paleo

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Healthy Pumpkin Bran Muffins from Natalie at Life Made Simple

These beauties pack a nutritional wallop! They’re turbo-loaded with whole-wheat flour, wheat bran, and flax … plus protein-rich Greek yogurt! Bonus: you just need one bowl!

•  Whole Wheat  

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Gluten Free Paleo Pumpkin Muffins with Almond Flour from Taylor at Food Faith Fitness

Secret ingredient alert here! (Psssst … it’s cashew butter.) Taylor says the cashew butter gives these muffins their “DENSE and chewy CRAVEABILITY that is going to make your inner texture freak just SO happy about muffins.” Geez … with a description like that, how can you not give these a try?!?

Gluten Free    Paleo    Dairy Free    Refined Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Grain-Free Chocolate Chip Pumpkin Muffins from Ann at Fountain Avenue Kitchen

This ingenious recipe doesn’t use any grains or flour at all. Not even coconut flour or almond flour! Yet, thanks to their unique combination of ingredients, Ann says they’re “wonderfully moist and have a slightly fudge-like texture.”

•  Gluten Free  

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Lowfat Pumpkin Muffin Top Recipe from Christi at Love from the Oven

Christi also offers an option for baking her recipe into actual muffins, but I thought the “muffin top” idea was just so darn cute!

Whole Wheat    Dairy Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Savory Pumpkin Muffins with Apple & Sage from Raia at Raia’s Recipes

I adore sage, especially in cozy fall recipes. (Remember my Pumpkin Hummus with Fresh Sage and my Spaghetti Squash with Sage-Browned Butter? Mmmmmm … sage). So I immediately fell in love with the idea for this unique pumpkin muffin recipe that’s all about savoriness and a creative autumn trio of pumpkin, apple and SAGE!

Gluten Free    Paleo    Dairy Free    Sugar Free

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From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

Pumpkin Banana Oat Muffins from Hope at Love Food Nourish

I’m so incredibly intrigued by the ingredients here, including bananas and dried dates for sweetness, tahini, and a medley of warm chai spices! Even more intriguing (and easy): Hope mixes these up entirely in her food processor. Brilliant!

Gluten Free    Dairy Free    Refined Sugar Free

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See … I told ya you’d be inspired!

Whip up one of these recipes for breakfast tomorrow, or surprise the kiddos with a nourishing after-school snack of warm, scrumptiously healthy pumpkin muffins! (And hey, feel free to FedEx me a couple while you’re at it!)

And if you just can’t get enough pumpkin everything … pop over to our list of the very best pumpkin BREAD recipes, too – lots more delicious things to bake this fall!

From paleo to gluten free, sugar free to whole grain! No matter what “healthy” means to you, we’ve got pumpkin muffins you’ll love! Unique flavor combos and lots of decadence … but so nutritious, too! These healthy pumpkin muffin recipes are easy to make – whip one up for quick breakfasts or healthy snacks! | pumpkin recipes | pumpkin muffins healthy | gluten free | grain free | paleo | whole wheat | refined sugar free | dairy free | #healthyrecipes #pumpkin #muffins | www.TwoHealthyKitchens.com

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