Healthy pumpkin chocolate chip muffins that actually fit your macros — and don’t taste like they’re trying to be healthy! 

I’ve made a lot of pumpkin muffins over the years trying to find the one that checks every box: moist enough to eat on its own, sweet enough to feel like a treat, and macro-friendly enough that I’m not rearranging my entire day around one muffin. This is that recipe.

These are made with whole wheat flour, Greek yogurt, and monk fruit — no added sugar — and each muffin comes in at 27 carbs, 5 fat, and 6 protein with 5 grams of fiber. That’s a legit snack or breakfast that doesn’t blow up your numbers. I make a batch and they’re gone within two days in this house, which tells you everything.

The Greek yogurt is what keeps them ridiculously moist without needing oil. The almond butter adds a subtle richness and depth without piling on fat. And the Lily’s sugar-free milk chocolate chips give you that melty chocolate in every bite without the sugar crash afterward. If you’ve ever had a “healthy” muffin that tasted like cardboard with good intentions, this isn’t that.

What I love most about this recipe is how forgiving it is. You don’t need a stand mixer or any special equipment — one bowl for dry, one for wet, fold together, and they’re in the oven. Twenty to twenty-five minutes later, you’ve got twelve muffins that are ready for the week. I usually make these on a Sunday and grab one with coffee every morning until they’re gone (which, again, is about two days because my boys have zero restraint when it comes to anything with chocolate chips).

The whole recipe is already logged in MyFitnessPal as RJF Healthy Pumpkin Chocolate Chip Muffins, so you can scan it and go. No guessing, no manual entry, no doing math at 6 AM.

healthy pumpkin chocolate chip muffins

Healthy Pumpkin Chocolate Chip Muffins

6g protein per muffin

25 minutes to make

14 ingredients

Makes 12 muffins

Ingredients

240g whole wheat flour (2 cups)

36g golden monk fruit (or sub brown sugar)

1 tsp baking soda

1.5 tsp cinnamon

1/2 tsp ground nutmeg

1/4 tsp ground cloves

1/4 tsp ground ginger

1.5 tsp vanilla

32g almond butter (2 tbsp)

120ml skim milk (1/2 cup)

170g nonfat, plain Greek yogurt (2/3 cup)

1 large egg

390g 100% pumpkin puree (15oz can minus 1/4 cup)

100g SF Lily’s milk chocolate chips

Directions

  • Preheat oven to 350 degrees.
  • Prep 12 muffin tins with paper liners and coat lightly with olive oil spray.
  • Add all dry ingredients to a large bowl — flour, monk fruit, baking soda, cinnamon, nutmeg, ginger, and cloves.
  • Add all wet ingredients to a medium bowl — almond butter, yogurt, vanilla, milk, pumpkin, and egg. Whisk to combine.
  • Slowly pour wet ingredients into dry ingredients and fold just to combine (don’t overmix).
  • Fold in 80g of the chocolate chips.
  • Pour into 12 muffin tins. Top each with 3-4 extra chocolate chips (a total of another 20g).
  • Bake for 20-25 minutes or just until a toothpick comes out clean.

Serve immediately or store in an airtight container for up to 5 days in the fridge.

If You're Looking For More

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Or, browse a few of my family-tested recipes that fit right into your week ⬇️

Nutrition Info

Search MyFitnessPal for:

RJF Healthy Pumpkin Chocolate Chip Muffins

Per Muffin:

177 calories

27g carbs | 5g fat | 6g protein

5g fiber

Makes 12 muffins

Rachel Jay Farrell intentional family living blog for faith-driven moms

I’m a mom of three who fell in love with nutrition and strength training after having kids. Now I create simple, high-protein recipes and healthy living ideas that help busy moms fuel their families well and make nourishing food a normal part of everyday life.

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