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!

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:

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

For the fruit, seeds, and extras:

• 1/2 cup sweetened shredded coconut
• 1/2 cup raisins, dried cranberries, and/or dried blueberries (1 1/2 to 2 cups mixed dried fruit such as figs or apricots)
• 2 cups grated carrot
• 1 shredded apple
• 1 can (8 oz) crushed pineapple, well drained
• 1/2 cup hulled sunflower seeds
• 1/2 cup pepitas (pumpkin seeds)
• 1/4 cup chia seeds
• 1/4 cup hemp hearts

For the wet mixture:

• 3 large eggs
• 2/3 cup vegetable or olive oil
• 1 tsp vanilla extract

Step 1: Combine Dry Ingredients

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

In a large mixing bowl, combine the multigrain flour, granulated sugar, ground cinnamon, baking powder, and salt.

Whisk or stir until everything is evenly distributed.

This forms the base of your muffin batter.

Step 2: Incorporate Fruits, Vegetables, Coconut, and Seeds

• 1/2 cup sweetened shredded coconut
• 1/2 cup raisins, dried cranberries, and/or dried blueberries (1 1/2 to 2 cups mixed dried fruit such as figs or apricots)
• 2 cups grated carrot
• 1 shredded apple
• 1 can (8 oz) crushed pineapple, well drained
• 1/2 cup hulled sunflower seeds
• 1/2 cup pepitas (pumpkin seeds)
• 1/4 cup chia seeds
• 1/4 cup hemp hearts

Add the sweetened shredded coconut, the combined dried fruit and raisins (or cranberries/blueberries), grated carrot, shredded apple, well-drained crushed pineapple, hulled sunflower seeds, pepitas, chia seeds, and hemp hearts into the bowl with your dry ingredients.

Stir everything together until the fruits, seeds, and veggies are evenly coated with the flour mixture.

Step 3: Mix Wet Ingredients

• 3 large eggs
• 2/3 cup vegetable or olive oil
• 1 tsp vanilla extract

In a separate medium-sized bowl, whisk together the eggs, vegetable or olive oil, and vanilla extract until smooth and well combined.

This mixture will help bind everything together once added to the dry ingredients.

I prefer olive oil for a subtle flavor, but vegetable oil works great too.

Step 4: Combine Wet and Dry Mixtures

• wet mixture from Step 3
• dry and fruit mixture from Steps 1 and 2

Pour the whisked wet mixture from Step 3 into the bowl of dry ingredients and fruit/seed mixture from Steps 1 and 2.

Stir gently but thoroughly until all ingredients are incorporated.

The batter will be very thick at this stage—don’t worry, that’s how it should be.

Step 5: Fill Muffin Cups and Bake

• thick muffin batter from Step 4

Spoon the thick batter into 12 lined or greased cupcake baking cups, filling each one heaping full, or use 16 cups for regular-size muffins.

Bake at 350°F (175°C) for 30-35 minutes, or until the tops are nicely browned and have a crusty look.

Let them cool slightly before enjoying.

For a little extra crunch, I sometimes sprinkle a few pepitas on top before baking.

Wholesome Pumpkin Muffins

Delicious Wholesome Pumpkin Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 16 minutes mins

Cook Time 34 minutes mins

Total Time 50 minutes mins

Servings 4

Calories 3200 kcal

Ingredients

  

For the dry blend:

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

For the fruit, seeds, and extras:

• 1/2 cup sweetened shredded coconut
• 1/2 cup raisins, dried cranberries, and/or dried blueberries (1 1/2 to 2 cups mixed dried fruit such as figs or apricots)
• 2 cups grated carrot
• 1 shredded apple
• 1 can (8 oz) crushed pineapple, well drained
• 1/2 cup hulled sunflower seeds
• 1/2 cup pepitas (pumpkin seeds)
• 1/4 cup chia seeds
• 1/4 cup hemp hearts

For the wet mixture:

• 3 large eggs
• 2/3 cup vegetable or olive oil
• 1 tsp vanilla extract

Instructions

 

• In a large mixing bowl, combine the multigrain flour, granulated sugar, ground cinnamon, baking powder, and salt. Whisk or stir until everything is evenly distributed. This forms the base of your muffin batter.
• Add the sweetened shredded coconut, the combined dried fruit and raisins (or cranberries/blueberries), grated carrot, shredded apple, well-drained crushed pineapple, hulled sunflower seeds, pepitas, chia seeds, and hemp hearts into the bowl with your dry ingredients. Stir everything together until the fruits, seeds, and veggies are evenly coated with the flour mixture.
• In a separate medium-sized bowl, whisk together the eggs, vegetable or olive oil, and vanilla extract until smooth and well combined. This mixture will help bind everything together once added to the dry ingredients. I prefer olive oil for a subtle flavor, but vegetable oil works great too.
• Pour the whisked wet mixture from Step 3 into the bowl of dry ingredients and fruit/seed mixture from Steps 1 and 2. Stir gently but thoroughly until all ingredients are incorporated. The batter will be very thick at this stage—don’t worry, that’s how it should be.
• Spoon the thick batter into 12 lined or greased cupcake baking cups, filling each one heaping full, or use 16 cups for regular-size muffins. Bake at 350°F (175°C) for 30-35 minutes, or until the tops are nicely browned and have a crusty look. Let them cool slightly before enjoying. For a little extra crunch, I sometimes sprinkle a few pepitas on top before baking.