Mini Pumpkin Muffins With Greek Yogurt are tiny, tender morning bites that actually taste like a treat—not sad cardboard. These mini muffins pack pumpkin spice, protein from Greek yogurt, and cozy fall flavor into one poppable package. Want breakfast your kids will ask for again? This is it.
Introduction to the recipe
You’ll love these because they balance nutrition and flavor without drama. The Greek yogurt keeps the crumb moist while the pumpkin adds natural sweetness and color. They work as breakfast, lunchbox treats, or a quick snack when you need something wholesome and satisfying. Ready in under 40 minutes, they’re perfect for busy mornings and meal prep.
What makes these muffins so irresistible?
Why do people fall for these little cakes every time?
- They stay moist for days thanks to the Greek yogurt and pumpkin.
- They deliver warm autumn spices—cinnamon and nutmeg—that feel nostalgic.
- The mini size makes them poppable and portion-controlled.
- They’re flexible: swap flours, add mix-ins, or swap maple for honey.
Bold tip: don’t overmix the batter—stir just until combined to keep the muffins tender.
Ingredients (with short descriptions)
Here’s what you need and why it matters.
- Pumpkin puree (1 cup): Use canned plain pumpkin for consistent results; it adds moisture and subtle sweetness.
- Greek yogurt (¼ cup): Adds protein and creaminess—key for texture.
- Maple syrup or honey (2/3 cup): Natural sweeteners that blend beautifully with pumpkin.
- Vegetable oil (¼ cup): Keeps muffins tender; you can use melted butter or coconut oil.
- Egg (1): Binds ingredients and adds structure.
- Vanilla extract (2 tsp): Rounds flavors and softens tang.
- Whole wheat flour (1 2/3 cups): Gives a nutty base; swap half for all-purpose if you want lighter muffins.
- Spices: ground cinnamon (1 tsp) and nutmeg (¼ tsp) for warm notes.
- Baking soda + baking powder (½ tsp each): Work together to give lift and lightness.
- Salt (½ tsp): Balances sweetness and enhances flavor.
Substitution note: For gluten-free, use a 1:1 gluten-free flour blend. For a dairy-free version, swap Greek yogurt with a thick plant-based yogurt—expect a slightly different texture.
Simple how-to (step-by-step)
Make these muffins without fuss.
- Preheat oven to 350°F (175°C) and line a mini muffin pan or use liners for easy removal.
- Mix wet ingredients: In a large bowl, whisk pumpkin puree, maple syrup (or honey), Greek yogurt, oil, egg, and vanilla until smooth.
- Combine dry: In another bowl, whisk flour, cinnamon, nutmeg, baking soda, baking powder, and salt.
- Fold together: Add dry ingredients to wet and stir just until combined—a few small lumps are fine. Don’t overmix.
- Scoop batter into mini cups, filling nearly to the top.
- Bake 18–20 minutes for mini muffins (check early) or follow the high-heat trick for regular-size muffins: 425°F for 5 minutes, then reduce to 350°F for 16 minutes.
- Cool in pan 10 minutes, then transfer to a rack.
The story behind the recipe
I used to assume “healthy muffin” meant sad cardboard. My kids agreed. Then I decided to stop subtracting and start replacing—swap processed sugar for maple syrup, use Greek yogurt for moisture and protein, and add pumpkin for flavor. The result? These muffins—tender, flavorful, and actually fun to eat. They stuck around in our rotation because they hit the trifecta: easy, portable, and kid-approved.
Pro tips for the best outcome
- Measure flour correctly. Spoon it into the cup and level—don’t pack. Too much flour dries muffins out.
- Mix gently. Overmixing develops gluten and makes muffins tough. Stir until barely combined.
- Test early. Start checking at 18 minutes for mini muffins. A toothpick should come out clean or with a few moist crumbs.
- Use fresh leavening. Replace baking soda/powder every 6–12 months for reliable rise.
- Cool properly. Let muffins rest in the pan for 10 minutes before transferring to prevent crumbling.
- Make them tall: For regular muffins, the quick high-temp trick creates bakery-style domes—425°F for 5 minutes, then lower to 350°F.
Bold tip: use full-fat Greek yogurt for the best texture and flavor.

Variations to try
Flexibility makes these muffins a keeper. Try one of these spins:
- Pumpkin Yogurt Muffins: Increase yogurt to ½ cup for extra tang and softness.
- Pumpkin Spinach Muffins: Fold in finely chopped cooked spinach for a sneaky veggie boost.
- Pumpkin Muffins With Yogurt & Berries: Fold in blueberries or diced apples for fruity pops.
- Add-ins: Mix in chocolate chips, chopped pecans, or raisins.
- Less sweet: Cut maple syrup to ½ cup and add a mashed banana for natural sweetness.
- Pumpkin Muffins For Baby: Reduce spices and use maple or applesauce; mash the muffin for tiny hands or mash into purees.
Want extra protein? Stir in a scoop of vanilla protein powder—just reduce flour slightly so the batter doesn’t dry out.
Best way to serve
Serve warm with a smear of almond butter or a dollop of Greek yogurt and a drizzle of honey. Pair with a warm latte or a cup of chai. For brunch, plate them alongside fruit salad and scrambled eggs for a balanced spread.
Looking for a snack idea? Pack two minis with a boiled egg for a protein-packed portable breakfast.
Quick tips for storage and leftovers
- Room temp: Store in an airtight container for up to 3 days. Line with a paper towel to absorb moisture.
- Refrigerate: Keep in the fridge for up to 1 week; bring to room temp or warm briefly before serving.
- Freeze: Wrap individually and freeze up to 3 months. Thaw on the counter or microwave for 10–15 seconds.
- Day-of crunch: Toast briefly to refresh texture and bring back that just-baked warmth.
Bold tip: freeze extras—they thaw fast and make mornings easier.
Common mistakes and how to avoid them
- Overmixing the batter—stir gently.
- Using too much flour—measure correctly.
- Ignoring oven differences—check early; ovens vary.
- Skipping the high-heat trick if you want bakery-style tops—don’t skip it for regular muffins.
Greek yogurt specifics: why it works
Greek yogurt adds tang, moisture, and protein while keeping crumb tender. The acidity reacts with baking soda to help lift the muffins. It also stretches the sweetness, meaning you can use less maple syrup and still enjoy great flavor.
Quick FAQ
Can I use all-purpose flour instead?
Yes—the muffins will be a touch lighter, but still delicious.
Can I use plain yogurt instead of Greek yogurt?
You can; the muffins may turn out slightly less dense and a bit more tender. If using regular yogurt, reduce milk or oil slightly.
Are these muffins kid-friendly?
Absolutely—these are perfect Pumpkin Breakfast Ideas For Kids. The spices are mild and you can reduce them further for younger palates.
How do I make pumpkin muffins less cakey and more moist?
Use full-fat Greek yogurt, don’t overbake, and avoid overmixing. Adding a tablespoon of oil helps too.
Can I make a large batch?
Yes—double or triple the recipe and freeze extras. They reheat well.
Nutrition & swaps for special diets
- For lower sugar, reduce maple syrup and add a mashed banana or apple sauce to maintain moisture.
- For vegan versions, try a flax egg and plant-based Greek-style yogurt—expect subtle texture changes.
- To boost fiber, stir in 2–3 tablespoons of ground flaxseed or chia.
Final thoughts
If you’ve been avoiding healthy muffins because you assume they’ll be bland, this recipe will change your mind. These Mini Pumpkin Muffins With Greek Yogurt deliver warm fall flavor, reliable moisture, and real staying power. They adapt beautifully—try Pumpkin Yogurt Muffins or slip spinach into the batter for a savory twist. Whether you need Easy Healthy Pumpkin Muffins for school mornings or a portable weekend brunch idea, these mini muffins do the job with charm.
Give them a whirl this weekend. Bake a tray, freeze half, and enjoy the relief of a smart, tasty breakfast that actually gets eaten. FYI, your kids (and you) might start requesting pumpkin muffins all season long—can’t say I blame you. IMO, these are the kind of muffins that make healthy feel indulgent.
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Mini Pumpkin Muffins With Greek Yogurt — Bite-Size Fall Breakfasts
- Prep Time: 13 minutes
- Cook Time: 27 minutes
- Total Time: 40 minutes
- Yield: 4 servings 1x
- Category: Breakfast
Description
A moist, wholesome muffin that’s easy to bake and perfect for breakfast or snack time.
Ingredients
- 1 cup canned pumpkin purée
- 2/3 cup maple syrup or honey
- 1/4 cup 2% Greek yogurt (plain or vanilla)
- 1/4 cup vegetable oil
- 1 large egg
- 2 teaspoons vanilla extract
- 1 2/3 cups whole wheat flour
- 1 teaspoon ground cinnamon
- 1/4 teaspoon ground nutmeg
- 1/2 teaspoon baking soda
- 1/2 teaspoon baking powder
- 1/2 teaspoon salt
Instructions
- Preheat the oven to 350°F (175°C). Line a muffin tin with paper liners or grease the cups lightly.
- In a large mixing bowl, whisk together the pumpkin purée, maple syrup (or honey), and the Greek yogurt until smooth. Add the oil, egg, and vanilla; whisk until the wet mixture is uniform.
- In a separate bowl, combine the whole wheat flour, cinnamon, nutmeg, baking soda, baking powder, and salt. Stir so the spices and leaveners distribute evenly.
- Pour the dry ingredients into the wet mixture. Gently fold with a spatula or spoon just until the flour is incorporated — the batter should remain a bit thick and slightly lumpy. Avoid overmixing to keep the muffins tender.
- Divide the batter among the prepared muffin cups, filling each almost to the top.
- Bake for about 18–20 minutes, or until the tops are set and a toothpick inserted into the center comes out clean or with a few moist crumbs. Start checking at 18 minutes since ovens vary.
- Let the muffins rest in the pan for 10 minutes, then transfer them to a wire rack to cool completely.
Notes
- Serving & storage suggestion
- Enjoy warm or at room temperature. Store cooled muffins in an airtight container at room temperature for up to 3 days or refrigerate for up to a week. For longer storage, freeze individually wrapped muffins for up to 3 months; thaw at room temperature or warm briefly in the microwave.
- Tip: If you prefer a lighter crumb, substitute half the whole wheat flour with all-purpose flour.