Healthy Pumpkin Muffins with Millet and Raisins

Healthy Pumpkin Muffins with millet, raisins, and toasted pumpkin seeds. These pumpkin muffins are made with wholegrain flour, real pumpkin purée, and plenty of spices. They’re sweet, crunchy, filling, delicious, and freezer friendly to boot. Make up a batch of pumpkin oatmeal muffins for breakfasts on the go or healthy snacks.

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healthy pumpkin muffins in a muffin tin with a small decorative pumpkin to the side

Do you smell that?

Hang on. Put your face a little closer to your screen. Close your eyes. Inhale deeply.

Smell it now??? That’s pumpkin spice, b*tches!

Of all of the muffins in my repertoire, this one is probably my favourite. They’re moist (deal with it) but also crunchy thanks to toasted millet. They’re perfectly spiced, and studded with raisins so practically every bite has a pop of sweetness.

They’re easy to stir together in one bowl and are freezer friendly. My favourite afternoon snack is one of these healthy pumpkin muffins with a couple of slices of strong cheese (trust me on this one) and a Pumpkin Chai Latte. Or a pumpkin muffin slathered with Pumpkin Seed Butter, which is meta like woah.

I’ve also heard they go great with hayrides and pumpkin patch visits and that kind of thing, but I’ll need someone to validate that hypothesis for me. Any volunteers?

Honestly, they’re the best pumpkin muffins. Make up a batch to keep on hand for holiday breakfasts, grab-and-go snacks, or to throw in your lunch box. Whatever. Just make ‘em.

canned pumpkin, flour, yogurt, sugar, eggs, oats, millet, pumpkin seeds, raisins, and spices on a grey background

What’s in these pumpkin muffins?  

Alright, gather up your ingredients and let’s get going! Here’s what you’ll need:

  • Pumpkin purée – I use homemade pumpkin purée when I have it on hand, but canned is totally fine too.
  • Millet – Those little crunchy pearls you probably think is bird seed.
  • Pumpkin seeds – Mooooooore crunch!
  • Oats – Because pumpkin oatmeal muffins are delicious.
  • Raisins – We’re doing this, ok?
  • Flour – I use white whole wheat flour in these babies.
  • Yogurt – Moisture! Tang!
  • Milk – More moisture!
  • Olive oil – Yes please.
  • Sugar – A bit of brown sugar, and we’ll discuss alternative sweeteners below.
  • Eggs – Two large ones to bind it up.
  • Spices – Ginger, cinnamon, and nutmeg are in the house.
  • Baking powder, baking soda, salt – Support crew bringing things home.

Do you need any special equipment for this recipe?

You’ll need a set of muffin tins. These are the ones I have, and they work great. 

You’ll also need a bowl to mix everything together, a whisk, and a spatula.

pumpkin seeds and millet being toasted in a small skillet

How do you make these muffins?

If you want to make the BEST pumpkin muffins, listen up! We’re going to go one bowl, but we are going to take the extra step of toasting the millet and pumpkin seeds. It’ll be worth it for the delicious nutty flavour and crunchy texture.

Step 1: Place a small skillet over medium heat. Do not add any oil!

Add the pumpkin seeds and millet to the dry skillet, and toast, stirring often, until they’re fragrant and nutty smelling. Remove from the heat and set aside to cool.

photo collage of healthy pumpkin muffins being made in a metal bowl

Step 2: In a large bowl, mix the pumpkin puree, eggs, yogurt, milk, and oil. Use a whisk to mix everything together.

Step 3: Add the brown sugar, flour, spices, baking powder, baking, soda, and salt to the same bowl.

Use your whisk to slightly mix the dry ingredients together, then mix them into the wet mix.

Do not over mix!

pumpkin muffin batter being mixed in a metal bowl

Step 4: Mix in the oats.

Step 5: Add the toasted millet, pumpkin seeds, and raisins to the pumpkin muffin batter. Lightly mix together.

pumpkin seeds, millet, and raisins being mixed into healthy pumpkin muffins

Step 6: Spoon the muffin mixture into prepared muffin tins (I grease mine with butter; a spray is fine too).

Sprinkle the tops with additional pumpkin seeds if desired.

unbaked pumpkin muffins

Step 7: Bake! These healthy pumpkin muffins will bake for about 20-25 minutes.

Step 8: When the muffins come out of them oven, let them sit for 5 minutes. Then, give them a gentle twist and tip up on their sides to cool completely.

That’s it! Your muffins are done!

healthy pumpkin muffins cooling in a muffin tin

Can I reduce the sugar in these muffins?

I’ve already reduced it as much as I feel is possible without impacting the taste and texture of the muffins, so I’d caution you against reducing it anymore.

If you’re looking to use an alternative sweetener, I have previously made these muffins using date syrup in place of the brown sugar. In the recipe below I’ve noted the quantity of date syrup should you want to swap. 

What’s the best way to store muffins?

I’m of the opinion that the best way to store muffins is in the freezer.

Once your muffins are completely cool, pop them into a freezer bag and toss them in the freezer. They’ll last up to 3 months that way.

I also think that when you’re making lower sugar muffins that they somehow get a bit sweeter once they’ve been frozen. In any case, I always store my muffins in the freezer, always and forever.

Alternately, your healthy pumpkin muffins will last about 3 days stored at room temperature in an air-tight container. 

a healthy pumpkin muffin split in half in front of a tin of pumpkin muffins

Can I make vegan pumpkin muffins?

I have never tried making this recipe vegan, but here’s what I recommend: 

  • Replace the eggs with your favourite vegan egg replacer
  • Replace the yogurt and milk with plant-based milk and a squeeze of lemon juice

If you do try making these muffins vegan, please let us know in the comments what you do and how they turn out. Alternatively, you could try this recipe for Vegan Pumpkin Muffins from My Darling Vegan

Can I use a different type of flour?

I have tested this recipe using white whole wheat flour, whole wheat pastry flour, and a blend of regular whole wheat and all-purpose flours. All of those have yielded good results.

I have not tested this recipe using gluten-free flour, so cannot speak to any substitutions. 

Hey Nutrition Lady, are these muffins healthy?

Well, friends, they’re certainly healthier than your average coffee shop muffin. The sugar is very reduced compared to most pumpkin muffins, there is a good amount of fiber, and thanks to the pumpkin seeds and millet, they’re a they are also a good source of other minerals including zinc, copper, and iron.

Additionally, pumpkin seeds are a good source of protein. Pumpkin, and other yellow fleshed winter squash, is jam packed full of carotenes, which is the compound ultimately responsible for their colour, and also is a pre-cursor to Vitamin A (you need that so you can see).

Pumpkin also contains dietary fibre, potassium, vitamin C, and manganese.

overhead photo of pumpkin muffins popped out of a muffin tin

Other recipes you might enjoy:

Sweet Potato Gingerbread Waffles
Pumpkin Overnight Oats
Naturally Sweetened Pumpkin Pie
Healthy Pumpkin Granola
Pumpkin Snickerdoodles

a healthy pumpkin muffin cut in half with pumpkin puree and a tray of muffins in the background
Print Pin
5 from 3 votes

Healthy Pumpkin Muffins with Millet and Raisins

Healthy Pumpkin Muffins with millet, raisins, and toasted pumpkin seeds. These pumpkin muffins are made with wholegrain flour, real pumpkin purée, and plenty of spices. They're sweet, crunchy, filling, and delicious.
Course Baking
Cuisine American
Keyword Pumpkin Muffins
Prep Time 15 minutes
Cook Time 25 minutes
Total Time 40 minutes
Servings 12
Calories 324kcal
Author Katie Trant



  • ½ cup millet toasted
  • ½ cup pumpkin seeds toasted
  • 2 large eggs
  • ½ cup extra virgin olive oil
  • 3/3 cup light brown muscovado sugar or 1/2 cup date syrup
  • 1 ½ cups pumpkin puree
  • ½ cup whole milk
  • ½ cup plain yoghurt
  • 1 ¾ cups whole wheat pastry flour or 1 cup whole wheat + ¾ cup all purpose
  • 2 tsp baking powder
  • 1 ½ tsp baking soda
  • ½ tsp sea salt
  • 1 tsp ground cinnamon
  • 1 tsp ground ginger
  • ¼ tsp freshly ground nutmeg
  • ½ cup rolled oats
  • ½ cup raisins


  • Preheat your oven to 350°F / 180°C.
  • Liberally grease 12 muffin cups (or 15 if you prefer slightly smaller muffins), or line with parchment muffin liners.
  • Set a small, dry frying pan over medium heat. Place the millet in, and toast for 5 minutes or so, until it is fragrant and nutty. Transfer the millet to a small bowl.
  • Set the same frying pan back on the heat, and now toast the pumpkin seeds for about 5 minutes, until fragrant and nutty. Set aside to cool.
  • In a large bowl, whisk the eggs together with the olive oil, brown sugar, milk, yoghurt, and pumpkin purée.
  • Add the whole-wheat pastry flour, baking powder, baking soda, sea salt, cinnamon, ginger, and nutmeg right on top of the wet mix. Use a whisk to gently mix together.
  • Stir the dry mix down into the wet until just barely combined.
  • Add the oats, and stir to combine.
  • Now fold the toasted millet, ¼ cup of toasted pumpkin seeds (reserve the rest for sprinkling on the muffin tops), and raisins into the muffin batter.
  • Spoon the batter evenly into the prepared muffin tins, then sprinkle the tops with the remaining toasted pumpkin seeds.
  • Set in the oven and bake for 20-25 minutes, until a toothpick inserted in the middle of a muffin comes out clean.
  • Remove from the oven and let cool in the muffin tins for 5 minutes before removing the muffins to a wire rack to cool completely.


  • Nutrition values are an estimate only


Calories: 324kcal | Carbohydrates: 48g | Protein: 7g | Fat: 13g | Saturated Fat: 2g | Cholesterol: 37mg | Sodium: 287mg | Potassium: 377mg | Fiber: 5g | Sugar: 20g | Vitamin A: 4844IU | Vitamin C: 2mg | Calcium: 101mg | Iron: 2mg


This recipe was originally published October 23, 2014. It was retested, re-photographed, and most recently updated on November 14, 2019.


  1. Emily says

    I made these last night and would make again. I love the millet crunch and that they are not super sweet. One note is that they made much more than 12 in my standard muffin tin (which is not a complaint!).

  2. Sandra Lea says

    I just made these and they are so moist and tender. I would maybe up the spices a little bit next time but otherwise they are great. Thanks for the recipe.

    • Katie Trant says

      Hi Azzah, I don’t post calorie counts for a variety of reasons, but there are a number of wonderful recipe calculators online you could enter the recipe in to find out.

  3. Isadora @ she likes food says

    It is crazy how sometimes we take for granted that we can walk into the grocery store anytime of year and find whatever produce we want. I hope you start seeing more squash soon! I have a big bag of millet in the cupboard and I’ve been trying to think of how to use it and I think I know how now! These muffins sound awesome 🙂

  4. Cammy says

    But could they possibly be better than orange earl grey millet muffins? I’ve eaten no less than 100 of those to date 🙂 I’ll give ’em a go and let you know.

    • Katie Trant says

      Definitely let us know! I’d recommend using a non-dairy milk with a touch of lemon juice for a buttermilk effect rather than trying a non-dairy yoghurt. Either way, let us know what you do and how they turn out for you 🙂

  5. Alissa says

    I’ve got my fingers crossed that Sweden gets it’s squash act together! I’m at least happy to see that you’re making good use of your limited selection. I’ve been wanting to experiment with adding some millet to baked goods for a while, and pumpkin muffins sound like the perfect way to go. I’ve got pumpkin puree stockpiled at this point, so these just might end up on my breakfast table this weekend.


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