Whole wheat pumpkin muffins

Last Updated on September 27, 2026 by Michelle

When I started milling my own flour and experimenting with whole wheat baking, muffins stumped me. They either wouldn’t rise, tasted awful, or were crumbly. Fast-forward a few years and a lot of almost-thrown-in-towels, and these whole wheat pumpkin muffins are now a highly-requested treat in my house.

Whole wheat pumpkin muffins

The brown sugar filing hovers perfectly in the center of these soft, just-sweet-enough pumpkin muffins. Then they’re all topped off with a crunchy-yet-soft streusel topping. Then the icing on the cake (literally!!) is the sweet maple glaze drizzled over the top.

If you don’t mill your own flour yet, no worries! (Although, I gotta ask… what’s stopping you?) This recipe will work well with regular ol’ all-purpose flour as well.

If you do mill your own fresh flour, definitely try this recipe with this spelt. (And use code SOULYRESTED to save 15%!) It’s such a delicious choice and I feel great knowing the farmer and exactly how it was grown.

Can whole wheat pumpkin muffins be healthy?

Even though these are definitely a treat, with the addition of whole wheat flour, these pumpkin streusel muffins are packed full of vitamins, minerals, and they’re also higher in protein and fiber than if they were made with white flour.

Fresh milled flour actually contains all three parts of the wheat berry, including the bran and germ, which are powerhouse foods! Learn more about fresh milled flour here: Why I started milling my own flour.

Bonus: these muffins are made with coconut sugar, a complex, all-natural sugar, which will leave you feeling more full and without the energy crash of junky refined sugars. Learn more about sugars here: The best sugars to use.

Are muffins healthy or unhealthy?

Because these muffins are made with all-natural sugars, freshly milled flour, and zero preservatives, they’re actually a healthy snack.

But I can’t say the same thing about the muffins you order at your favorite coffee shop, or the ones you pick up in the grocery story bakery. Those have to stay moist and fresh for days (heck, sometimes weeks), so they’re loaded with all these preservatives I can’t pronounce, from mono and diglycerides, to sodium stearoyl lactylate, sorbitan monostearate, polysorbate 60, gelatinized wheat starch, and carnauba wax.

I don’t think you have to have a degree in food science to know which option is going to be a much better choice.

Bonus: these homemade muffins genuinely taste better.

How to make whole wheat pumpkin muffins with a brown sugar filling

Cocoa powder is my secret weapon for making your muffin filling more visible (and we all know your tastebuds start with your eyes!). You don’t taste the chocolate flavor since there’s not much cocoa powder in the filling, but it’s just enough to allow the bright color of the filling to shine throughout the muffin. Swirling the filling through the batter just allows the filling to stay put and not remain a dry lump of sugar, but instead transform into a gooey, lovely filling while the muffins bake.

Whole wheat pumpkin muffins recipe

INGREDIENTS

Streusel topping:

• 1/3 cup coconut sugar
• 3/4 cup (83 grams) spelt flour*
• 1 teaspoon ground cinnamon
• 4 tablespoons melted butter, lard, or coconut oil

Brown sugar filling:

• 1/3 cup coconut sugar
• 1.5 teaspoons ground cinnamon
• 1 teaspoon cacao powder (for color)
• 1 teaspoon sorghum syrup (or molasses)

Pumpkin muffin batter:

• 1/3 cup avocado oil, or other neutral-flavored oil
• 1 cup pumpkin puree
• 1 cup coconut sugar
• 2 eggs
• 1 teaspoon ground cinnamon
• 1/4 teaspoon ground ginger powder
• 1/4 teaspoon ground nutmeg
• generous pinch salt
• 2 teaspoons baking powder
• 1 1/2 cups (165 grams) spelt flour*

Maple glaze:

• 4 tablespoons maple syrup
• 2 tablespoons powdered sugar (or until desired consistency)

DIRECTIONS

1. First, if you’re milling your own fresh flour, mill about 250 grams of spelt wheat berries.
2. Mix the streusel topping. Combine the dry ingredients, then pour in the melted butter and stir until a moist crumble forms. Set in the fridge to cool.
3. Next mix the brown sugar filling. Combine everything in a small bowl, incorporating the molasses as best you can–some chunks are ok. Set aside.
4. For the pumpkin muffin batter, combine everything but the flour into a large mixing bowl, and mix until combined. Add the flour and stir until just combined.
5. Assemble the muffins by filling each hole of a muffin tray 1/2 full of batter (I find half a muffin is about 1 tablespoon). This recipe should make exactly 12 muffins, so fill 12 holes 1/2 way. Then sprinkle the brown sugar filling mixture evenly over all 12 muffins. Cover that with the remaining muffin batter so each muffin is filled. Carefully swirl a toothpick through each muffin to settle the filling into the batter, but don’t overmix.
6. Generously sprinkle the streusel topping over all the muffins.
7. Bake at 350 for 25 minutes, or until the internal temperature in the middle of the muffins reads about 200 degrees.
8. Set them aside to cool slightly, and mix the maple syrup and powdered sugar until it’s thick but drizzle-able.
9. When the muffins are mostly cool, drizzle the maple glaze all over the tops and enjoy!

*I like to use fresh milled spelt flour for both the streusel topping and the batter. You could also use barley or any soft wheat.

Some of the Important Ingredients

* I source many of my ingredients directly from this amazing food supplier; Use code SOULYRESTED for 15% off your entire first order of $100 or more with Azure Standard, delivered to a drop near you.

A few grain mills I use and recommend

If you’re considering investing in a grain mill, find out the questions you need to ask in the Ultimate Guide to Choosing a Grain Mill.

More like whole wheat pumpkin muffins:

• Wheat berries: everything you need to know
• Kamut chocolate chip cookies
• Fluffy 100% whole wheat dinner rolls
• Lasagna noodles with fresh milled flour
• Why I started milling my own flour

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