Wholesome Pumpkin Muffins

I was well into my thirties before I realized that muffins didn’t have to be loaded with sugar and butter to taste good. Growing up, the only muffins we had were the giant bakery ones that were basically cupcakes without frosting.

That’s because I didn’t know you could swap out half the oil for pumpkin puree and still get moist, fluffy muffins. Pumpkin muffins made the traditional way are pretty heavy and sweet. But when you use pumpkin as your secret ingredient, you get all the flavor with way less guilt.

What Kind of Multi Grain Flour Should I Use?

Multi grain flour is the foundation of these healthy muffins, and you have several good options to choose from. You can find pre-made multi grain flour blends at most grocery stores, which typically combine wheat flour with grains like oats, barley, and sometimes seeds. If you can’t find multi grain flour, you can easily make your own by mixing whole wheat flour with rolled oats, a bit of cornmeal, or even some ground flaxseed. Regular all-purpose flour will work in a pinch, but you’ll miss out on the extra fiber and nutty flavor that makes these muffins so hearty. Just keep in mind that different flour blends may absorb liquid differently, so you might need to adjust the wet ingredients slightly if your batter seems too thick or thin.

Options for Substitutions

These muffins are super forgiving and you can easily swap ingredients based on what you have in your pantry:

• Multi grain flour: All-purpose flour works perfectly fine, or try whole wheat flour for extra fiber. You can even use a gluten-free flour blend if needed – just add an extra tablespoon or two if the batter seems too wet.
• Dried fruits: Mix and match any dried fruits you like! Chopped dates, dried cherries, or even mini chocolate chips work great. Just keep the total amount around 1½ to 2 cups.
• Seeds: Don’t stress if you don’t have all the seeds listed. You can use just one type, like sunflower seeds, or swap in chopped walnuts or pecans instead. The total amount should stay around ¾ cup.
• Grated carrots: Zucchini works as a great substitute – just make sure to squeeze out excess moisture with a clean kitchen towel first.
• Vegetable oil: Melted coconut oil, applesauce, or even mashed banana can replace some or all of the oil for a different texture and flavor.
• Crushed pineapple: If you skip the pineapple, add an extra ½ cup of shredded apple or carrot to keep the muffins moist.

Watch Out for These Mistakes While Baking

The biggest mistake when making these healthy pumpkin muffins is not draining the crushed pineapple thoroughly – excess liquid will make your muffins dense and soggy, so press it through a fine mesh strainer or squeeze it in paper towels until barely any juice comes out. Another common error is overmixing the batter once you add the wet ingredients to the dry ones, which can result in tough, dense muffins instead of light and fluffy ones – just stir until the ingredients are barely combined. Don’t forget to coat your dried fruits and seeds in a little flour before folding them in, as this prevents them from sinking to the bottom during baking. Finally, avoid overpacking your muffin cups since these are loaded with mix-ins that expand during baking – fill them about 2/3 full for the best rise and texture.

What to Serve With Pumpkin Muffins?

These hearty pumpkin muffins are packed with so much good stuff that they’re practically a meal on their own, but they pair beautifully with your morning coffee or afternoon tea. I love serving them alongside a dollop of Greek yogurt or cream cheese for extra richness, especially since the muffins have all those seeds and dried fruits for texture. They also make a great breakfast when you spread a little almond butter or peanut butter on top for added protein. For a cozy fall treat, try warming them up slightly and serving with a drizzle of honey or maple syrup.

Storage Instructions

Keep Fresh: These healthy pumpkin muffins stay moist and delicious when stored in an airtight container at room temperature for up to 4 days. The dried fruits and seeds actually help keep them from drying out, which is one of my favorite things about this recipe!

Freeze: I love freezing these muffins for quick breakfasts throughout the month. Wrap each muffin individually in plastic wrap or store them in a freezer-safe container for up to 3 months. They thaw perfectly and taste just as good as fresh.

Enjoy: To enjoy frozen muffins, just let them thaw at room temperature for about 30 minutes, or pop them in the microwave for 20-30 seconds. You can also warm them in a 300°F oven for 5-10 minutes if you prefer them toasty. They’re honestly great cold too, especially on busy mornings!

Preparation Time	15-20 minutes
Cooking Time	30-35 minutes
Total Time	45-55 minutes
Level of Difficulty	Medium

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 3050-3350
• Protein: 50-60 g
• Fat: 140-160 g
• Carbohydrates: 430-470 g

Ingredients

For the dry blend:

• 1 tbsp ground cinnamon (freshly ground preferred for more flavor)
• 2 cups multigrain flour (I use King Arthur multigrain blend)
• 1/2 tsp salt
• 3/4 cup sugar
• 2 tsp baking powder

For the fruit, seeds, and extras:

• 2 cups grated carrot (finely shredded for even distribution)
• 1/2 cup dried fruit (raisins, cranberries, blueberries, figs, or apricots)
• 1/2 cup pepitas
• 1/2 cup hulled sunflower seeds
• 1 shredded apple (about 1 medium apple, shredded fine)
• 1/2 cup sweetened shredded coconut
• 1/4 cup hemp hearts (adds nutrition and nutty flavor)
• 1 can crushed pineapple, well drained (I use Dole)
• 1/4 cup chia seeds

For the wet mixture:

• 3 large eggs (room temperature)
• 1 tsp vanilla extract
• 2/3 cup vegetable oil (or any neutral oil like canola)

Step 1: Prepare Mise en Place and Combine Dry Ingredients

• 2 cups multigrain flour
• 3/4 cup sugar
• 1 tbsp ground cinnamon
• 2 tsp baking powder
• 1/2 tsp salt

Start by measuring out all your ingredients and preparing them for mixing.

Combine the multigrain flour, sugar, ground cinnamon, baking powder, and salt in a large mixing bowl, whisking them together thoroughly to distribute the leavening agents and cinnamon evenly throughout the flour—this prevents clumps of cinnamon in your finished muffins.

I prefer freshly ground cinnamon here because it has a brighter, more complex flavor than pre-ground, which really elevates these wholesome muffins.

Step 2: Add Mix-Ins to Dry Ingredients

• 1/2 cup sweetened shredded coconut
• 1/2 cup dried fruit
• 2 cups grated carrot
• 1 shredded apple
• 1 can crushed pineapple, well drained
• 1/2 cup hulled sunflower seeds
• 1/2 cup pepitas
• 1/4 cup chia seeds
• 1/4 cup hemp hearts

Add the shredded coconut, dried fruit, finely shredded carrot, shredded apple, well-drained crushed pineapple, sunflower seeds, pepitas, chia seeds, and hemp hearts to the dry mixture.

Stir everything together until the wet ingredients (carrot, apple, and pineapple) are evenly distributed throughout—this prevents clumping and ensures every muffin gets a balanced combination of flavors and textures.

The moisture from the shredded vegetables and fruit will start to hydrate slightly, which is fine at this stage.

Step 3: Whisk Wet Ingredients Together

• 3 large eggs, room temperature
• 2/3 cup vegetable oil
• 1 tsp vanilla extract

In a separate bowl, whisk together the room-temperature eggs, vegetable oil, and vanilla extract until well combined and slightly emulsified.

Room-temperature eggs incorporate more easily into the batter and create a better texture in the finished muffins.

Whisk for about 30 seconds until the mixture looks slightly creamy and uniform.

Step 4: Combine Wet and Dry Mixtures

• wet ingredient mixture from Step 3
• dry ingredient mixture with mix-ins from Step 2

Pour the wet ingredient mixture from Step 3 into the dry mixture from Step 2.

Fold everything together gently with a spatula just until combined—don’t overmix.

The batter should look slightly lumpy and shaggy; overmixing develops gluten and creates tough, dense muffins.

A few streaks of dry flour are fine and actually preferable to a smooth, fully incorporated batter.

Step 5: Fill Muffin Cups and Bake

• batter from Step 4

Preheat your oven to 350°F while you prepare your muffin tin.

Line 12-16 muffin cups with paper liners or lightly grease them with neutral oil.

Divide the batter evenly among the cups, filling each about two-thirds to three-quarters full—this leaves room for the muffins to rise without overflowing.

Bake at 350°F for 30-35 minutes, until a toothpick inserted into the center of a muffin comes out clean or with just a few moist crumbs.

Let the muffins cool in the tin for 5 minutes before turning them out onto a wire rack.