
This naturally sweet pumpkin chocolate chip muffin recipe brings the perfect balance of spices, creamy almond butter, and melty chocolate chips for a snack that will disappear quickly. These muffins are moist and tender with a rich flavor that makes them suitable for breakfast or as an afternoon treat alongside your favorite hot beverage.
I first created these muffins when looking for ways to use leftover pumpkin puree during fall baking season. My kitchen filled with the most incredible aroma of spices and chocolate, and since then they've become our go to weekend breakfast treat that everyone requests by name.
Ingredients
- Whole wheat flour provides hearty texture and nutty flavor while adding fiber
- Baking soda and powder work together for the perfect rise and tender crumb
- Cinnamon and pumpkin pie spice create that classic warm fall flavor profile
- Eggs bind everything together and provide structure
- Pumpkin puree adds moisture and subtle earthy sweetness
- Almond butter creates richness and keeps muffins tender for days
- Brown sugar or coconut sugar adds caramel notes that pair perfectly with the spices
- Almond milk keeps the batter at the right consistency without dairy
- Vanilla extract enhances all the other flavors
- Dark chocolate chips provide pockets of melty goodness throughout each muffin
Step-by-Step Instructions
- Prepare Your Oven and Pan
- Preheat your oven to 175°C or 350°F to ensure it reaches the proper temperature. Line your muffin tin with paper liners or use a light coating of oil to prevent sticking. Taking this step first ensures your oven is hot and ready when your batter is mixed.
- Mix the Dry Ingredients
- Combine the flour, baking soda, baking powder, cinnamon, pumpkin pie spice, and salt in a medium bowl. Whisk thoroughly to distribute the leavening agents and spices evenly throughout the flour. This prevents clumps of spice or baking soda in your finished muffins.
- Blend the Wet Ingredients
- In a larger bowl, whisk together eggs, pumpkin puree, almond butter, sugar, almond milk, and vanilla until completely smooth. The almond butter might be thick, so take your time here to ensure it incorporates fully with no streaks remaining. The mixture should be uniform in color and consistency.
- Combine Wet and Dry Mixtures
- Add the dry ingredients to the wet ingredients and fold gently with a spatula just until no dry flour remains visible. Use a light hand here and stop mixing as soon as the ingredients are combined. Overmixing develops gluten which can make your muffins tough instead of tender.
- Add Chocolate Chips
- Gently fold in the chocolate chips, distributing them evenly throughout the batter. This ensures every muffin gets plenty of chocolate without overmixing the batter. Save a small handful to sprinkle on top if desired.
- Fill Muffin Cups and Bake
- Divide the batter evenly among your prepared muffin cups, filling each about three quarters full. If using, sprinkle the tops with additional chocolate chips, chopped almonds, or pumpkin seeds. Bake for 18 to 20 minutes until the tops spring back when lightly touched and a toothpick inserted into the center comes out clean or with just a few moist crumbs.

The almond butter is truly the secret ingredient that takes these muffins from good to exceptional. I discovered this trick by accident when I was out of oil one day and needed a substitute. The rich nutty flavor complements the pumpkin perfectly while adding nutritional value and keeping the texture incredibly moist.
Make Ahead and Storage
These muffins actually improve in flavor after sitting overnight as the spices meld together. Store them in an airtight container at room temperature for up to 3 days. For longer storage, place them in a freezer safe container with parchment between layers and freeze for up to 2 months. Thaw overnight in the refrigerator or microwave individual muffins for about 30 seconds when you need a quick snack.
Perfect Substitutions
If you need to make these muffins nut free, sunflower seed butter works beautifully in place of almond butter though it may turn the muffins slightly green due to a natural reaction with baking soda. For a gluten free version, substitute a 1 to 1 gluten free baking blend for the whole wheat flour. The muffins can easily be made vegan by replacing the eggs with flax eggs combine 2 tablespoons ground flaxseed with 6 tablespoons water and let sit for 5 minutes until gelatinous.
Serving Suggestions
These muffins make a complete breakfast paired with Greek yogurt and fresh fruit. For an extra special treat, warm a muffin slightly and spread with a thin layer of additional almond butter or cream cheese. They also pair wonderfully with hot apple cider or a pumpkin spice latte for the ultimate fall treat.
The Nutritional Benefits
Pumpkin is an excellent source of vitamin A and antioxidants while being naturally low in calories. The addition of almond butter provides healthy fats and protein that help keep you satisfied longer than traditional muffins. Using whole wheat flour adds fiber and nutrients that are stripped from white flour. These thoughtful ingredient choices create a treat that satisfies sweet cravings while providing nutritional benefits.

Common Questions
- → Can I make these muffins gluten-free?
Yes! Simply substitute the whole wheat or all-purpose flour with your preferred gluten-free flour blend. For best results, use a 1:1 gluten-free baking mix that contains xanthan gum to maintain proper texture and rise.
- → How can I store these pumpkin chocolate chip muffins?
Store the muffins in an airtight container at room temperature for 2-3 days. For longer storage, freeze them for up to 2 months. To enjoy a frozen muffin, thaw at room temperature or microwave for 20-30 seconds.
- → Can I substitute the almond butter with another nut butter?
Absolutely! Cashew butter creates a milder flavor profile, while peanut butter adds a more distinctive taste. Sunflower seed butter works well for those with nut allergies. Just ensure your substitute has a similar consistency to almond butter.
- → What can I use instead of pumpkin pie spice?
If you don't have pumpkin pie spice, you can make your own by combining ¼ teaspoon ground nutmeg and ¼ teaspoon ground ginger. Alternatively, a pinch of cloves and allspice added to cinnamon creates a similar warming flavor profile.
- → How can I make these muffins vegan?
To make these muffins vegan, replace the eggs with flax eggs (2 tablespoons ground flaxseed mixed with 5 tablespoons water, left to thicken for 5 minutes). Ensure your chocolate chips are dairy-free, and continue using plant-based milk as specified in the recipe.
- → Can I reduce the sugar content in these muffins?
Yes, you can reduce the sugar to ⅓ cup without significantly affecting the texture. You might also consider using mashed ripe banana or unsweetened applesauce to replace some of the sugar while maintaining moisture and adding natural sweetness.