
These pumpkin chocolate chip muffins with almond butter transform ordinary mornings into something special. The combination of earthy pumpkin, rich almond butter, and sweet chocolate chips creates a perfectly balanced treat that's surprisingly healthy. I've perfected this recipe over several fall seasons, gradually adjusting the spice levels and sweetness until it hit that ideal balance of indulgence and nutrition.
After making these countless times, I've found my family reaches for these muffins before store-bought treats. My teenage son actually requests these before his morning basketball practices, which feels like a major win in the nutrition department.
Ingredients (and why they matter)
- 1 cup almond butter: Creates a moist, tender crumb while adding protein and healthy fats. Look for varieties with no added sugar and a smooth consistency.
- 1 cup canned pumpkin: Provides moisture, fiber, and that distinctive fall flavor. Choose 100% pure pumpkin, not pumpkin pie filling.
- 2 eggs: Act as binders that help the muffins rise and hold together. Room temperature eggs incorporate more evenly.
- 1/4 cup honey: Offers natural sweetness with subtle floral notes. Local raw honey provides the best flavor.
- 1 tsp vanilla extract: Enhances all the other flavors. Pure extract rather than imitation makes a noticeable difference.
- 1 cup almond flour: Creates structure without gluten. Select blanched, fine-ground almond flour for the best texture.
- 1 tsp baking powder: Provides necessary lift. Check that yours is fresh (less than 6 months old) for proper rising.
- 1/2 tsp cinnamon: Adds warmth and complements the pumpkin perfectly. Saigon cinnamon has the strongest flavor.
- 1/4 tsp nutmeg: Contributes a distinctive autumnal note. Freshly grated nutmeg is worth the extra effort.
- 1/2 cup mini chocolate chips: Distribute more evenly than regular chips, ensuring chocolate in every bite. Dark chocolate chips reduce overall sweetness while adding antioxidants.
Step-by-Step Instructions
- Step 1: Prepare Your Equipment
- First, preheat your oven to 350°F (175°C). This temperature is crucial for proper rising without over-browning the muffins. While the oven heats, line a standard 12-cup muffin tin with paper liners. I've found unbleached parchment liners work best as the muffins tend to stick less to them than to regular paper liners. If you don't have liners, you can grease the tin thoroughly with coconut oil.
- Step 2: Mix Wet Ingredients
- In a large mixing bowl, combine the almond butter and pumpkin first, stirring until completely smooth. This initial blending is important because almond butter can be stubborn about incorporating. Once smooth, add your eggs one at a time, mixing well after each addition. The mixture should become lighter in color and slightly fluffier. Finally, add the honey and vanilla extract, stirring until the mixture looks uniform with no streaks.
- Step 3: Combine Dry Ingredients
- In a separate, smaller bowl, whisk together your almond flour, baking powder, cinnamon, and nutmeg. Whisking these ingredients separately ensures even distribution of the leavening agent and spices. This prevents pockets of baking powder or intense spice in your finished muffins. Take a moment to break up any clumps in the almond flour by pressing them against the side of the bowl with your whisk or spoon.
- Step 4: Create Your Batter
- Gradually add the dry mixture to your wet ingredients, folding gently with a silicone spatula or wooden spoon rather than vigorously stirring. This gentle folding preserves the air in the batter, leading to lighter muffins. Mix just until no dry spots remain – overmixing will make your muffins dense. Once combined, fold in the mini chocolate chips using just a few strokes to distribute them evenly.
- Step 5: Fill Muffin Cups
- Using a scoop or spoon, divide the batter evenly among your prepared muffin cups. They should be about 3/4 full – this leaves enough room for rising without overflowing. If you have a few empty cups in your tin, fill them halfway with water to ensure even baking and prevent the pan from warping.
- Step 6: Bake to Perfection
- Place the muffin tin in the center of your preheated oven and bake for 18-20 minutes. You'll know they're done when the tops are slightly domed and spring back when lightly touched, and a toothpick inserted into the center comes out clean or with just a few moist crumbs (chocolate smears are okay). Resist opening the oven during the first 15 minutes of baking to prevent them from sinking.
- Step 7: Cool Properly
- Remove the muffins from the oven and let them rest in the tin for about 5 minutes. This brief resting period allows them to set up and makes removal easier. Then transfer them to a wire cooling rack to cool completely. Even though it's tempting to eat them warm, the texture actually improves as they cool, becoming more cohesive.

I discovered the power of almond butter in baking when my daughter developed a sensitivity to dairy. The rich, nutty flavor works wonderfully in these muffins, and my husband—who typically avoids "healthy" baked goods—can't tell the difference. He grabs one every morning with his coffee and says they keep him full until lunch, unlike regular muffins that leave him hungry an hour later.
The Magic of Spice Variations
These muffins serve as an excellent canvas for different spice combinations. While the classic cinnamon-nutmeg duo works beautifully, I've experimented with cardamom, ginger, and even a pinch of cloves. The warmer the spice blend, the more these muffins taste like fall. My personal favorite combination adds 1/4 teaspoon of cardamom alongside the listed spices—it brings an unexpected complexity that pairs wonderfully with the chocolate. Don't be afraid to adjust the spice levels gradually until you find your family's perfect balance. Remember that spices lose potency over time, so if yours have been sitting in the cabinet for more than a year, you might need to increase the amounts slightly.
Storage and Make-Ahead Tips
Proper storage makes a significant difference in maintaining the texture and flavor of these muffins. Once completely cooled, store them in an airtight container at room temperature for up to three days. The natural moisture from the pumpkin and almond butter keeps them fresh longer than traditional flour-based muffins. For longer storage, place them in a freezer-safe container with parchment paper between layers and freeze for up to three months. To enjoy a frozen muffin, either thaw overnight in the refrigerator or microwave for 20-30 seconds. I often make a double batch specifically for freezing, which provides quick breakfasts on hectic mornings or last-minute snacks when unexpected guests arrive.

Nutritional Benefits Beyond Taste
These muffins aren't just delicious—they're nutritional powerhouses compared to conventional baked goods. The almond flour and almond butter provide heart-healthy monounsaturated fats, which help maintain healthy cholesterol levels. Pumpkin delivers a substantial dose of vitamin A and fiber, supporting both eye health and digestive function. By using honey instead of refined sugar, you're introducing beneficial enzymes and antioxidants while providing a more stable energy source. This nutritional profile makes these muffins an excellent option for active individuals, growing children, or anyone looking to incorporate more nutrient-dense foods into their diet. My nutrition-conscious sister-in-law was surprised to learn these muffins contain approximately half the sugar of traditional recipes while delivering triple the protein and fiber.
Frequently Asked Questions
- → What can I use instead of almond butter?
You can substitute peanut butter, cashew butter, or sunflower seed butter for almond butter based on your preference or dietary needs.
- → Can I make these muffins gluten-free?
Yes! These muffins are naturally gluten-free since they use almond flour instead of traditional wheat flour.
- → How do I store these muffins?
Store them in an airtight container at room temperature for up to 3 days, or refrigerate for up to a week to extend freshness.
- → Can I freeze the muffins for later?
Absolutely! Freeze the muffins in a sealed container for up to 3 months. Thaw overnight at room temperature or in the refrigerator.
- → Can I replace chocolate chips with something else?
Yes, you can use chopped nuts, dried fruits like raisins or cranberries, or leave them out entirely for a simpler muffin.
- → What can I use instead of honey?
If you prefer an alternative to honey, you can substitute maple syrup or agave nectar for a similar sweetness profile.