These Pumpkin Seed and Flax Muffins offer a delicious and nutritious way to start your day. You’ll love how easy they are to make, providing a healthy breakfast option everyone can enjoy. This recipe is perfect for those seeking healthy breakfast muffins that are both satisfying and good for you.
Key Ingredients & Substitutions
- Pumpkin puree: Use canned pumpkin, not pumpkin pie filling.
- Flaxseed meal: Essential for binding and nutrition. You can grind whole flaxseeds if needed.
- Whole wheat flour: Provides fiber. You can use all-purpose flour for a lighter texture.
- Maple syrup: Natural sweetener. Honey or agave nectar are good alternatives.
- Pumpkin seeds: Adds a delightful crunch. Sunflower seeds work well too.
Ingredients
Main Ingredients:
- 1 ½ cups whole wheat flour
- ½ cup flaxseed meal
- ½ cup packed light brown sugar
- 1 teaspoon baking soda
- ½ teaspoon ground cinnamon
- ¼ teaspoon ground nutmeg
- ½ teaspoon salt
- 1 cup pumpkin puree
- ½ cup plant-based milk (almond, soy, or oat milk work great)
- ¼ cup maple syrup
- ¼ cup vegetable oil (or melted coconut oil)
- 1 teaspoon vanilla extract
- ½ cup pumpkin seeds (plus extra for topping)
How Much Time Will You Need?
- Total Time: 35 minutes
- Prep Time: 15 minutes
- Cook Time: 20 minutes
- Servings: 12 healthy breakfast muffins
- Calories per serving: Approximately 220 calories
- Tools Needed: Muffin tin, paper liners, two large mixing bowls, whisk, spatula.
Step-by-Step Instructions
1. Prepare Your Oven and Muffin Tin
Preheat your oven to 375°F (190°C). Line a 12-cup muffin tin with paper liners or lightly grease each cup. This ensures your healthy breakfast muffins won’t stick.
2. Combine Dry Ingredients
In a large bowl, whisk together the whole wheat flour, flaxseed meal, brown sugar, baking soda, cinnamon, nutmeg, and salt. Make sure there are no lumps for evenly baked muffins.
3. Mix Wet Ingredients
In a separate large bowl, whisk together the pumpkin puree, plant-based milk, maple syrup, vegetable oil, and vanilla extract. Combine these thoroughly until smooth.
4. Combine Wet and Dry Mixtures
Pour the wet ingredients into the dry ingredients. Stir gently with a spatula until just combined. Be careful not to overmix, as this can lead to tough muffins.
5. Fold in Pumpkin Seeds
Gently fold in ½ cup of pumpkin seeds into the batter. Distribute them evenly throughout for a satisfying crunch in every bite of your healthy breakfast muffins.
6. Fill Muffin Cups
Divide the batter evenly among the 12 prepared muffin cups. Sprinkle the remaining pumpkin seeds on top of each muffin for a pretty finish.
7. Bake the Muffins
Bake for 18-22 minutes, or until a toothpick inserted into the center of a muffin comes out clean. Allow them to cool in the muffin tin for a few minutes before transferring to a wire rack.
Variation Ideas
- Add dried fruit: Include ¼ cup of cranberries or chopped dates for extra sweetness.
- Spice it up: Add a pinch of ground ginger or cloves to the dry ingredients.
- Chocolate chip version: Stir in ½ cup of mini dairy-free chocolate chips.
- Nutty twist: Replace some pumpkin seeds with chopped walnuts or pecans.
Storage Instructions
Store your Pumpkin Seed and Flax Muffins in an airtight container at room temperature for up to 3 days. For longer storage, freeze them in a freezer-safe bag for up to 3 months. Thaw at room temperature or reheat briefly in the microwave.
Frequently Asked Questions (FAQ)
Q: Can you make these muffins gluten-free?
A: Yes, you can substitute the whole wheat flour with a 1:1 gluten-free baking blend.
Q: What if you don’t have flaxseed meal?
A: You can grind whole flaxseeds in a coffee grinder or food processor until they form a meal.
Q: Are these muffins suitable for meal prepping?
A: Absolutely! They make excellent healthy breakfast muffins to prepare ahead for busy mornings.
Q: Can you reduce the sugar content?
A: You can slightly reduce the brown sugar or maple syrup, but it might affect the texture and moisture.
Q: How do you know when the muffins are fully baked?
A: Insert a toothpick into the center; if it comes out clean with no wet batter, they are done.
Q: What is the best way to keep these muffins moist?
A: Avoid overmixing the batter, and store them in an airtight container once cooled.

