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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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, friends!
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? Be sure to check our archive of Pumpkin Recipes for more inspiration!
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.
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.
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.
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!
Step 4: Mix in the oats.
Step 5: Add the toasted millet, pumpkin seeds, and raisins to the pumpkin muffin batter. Lightly mix together.
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.
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!
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.
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.
Other recipes you might enjoy:
Healthy Pumpkin Muffins with Millet and Raisins
- ½ cup millet toasted
- ½ cup pumpkin seeds toasted
- 2 large eggs
- ½ cup extra virgin olive oil
- ¾ cup light brown muscovado sugar or ½ 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 teaspoon baking powder
- 1 ½ teaspoon baking soda
- ½ teaspoon sea salt
- 1 teaspoon ground cinnamon
- 1 teaspoon ground ginger
- ¼ teaspoon 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
This recipe was originally published October 23, 2014. It was retested, re-photographed, and most recently updated on November 14, 2019.