Healthy Apple Spice Mini Muffins
These healthy apple spice mini muffins are naturally sweetened with apples, butternut squash, and raisins for a soft, tender texture little ones love. Made with whole wheat pastry flour and warm fall spices, they’re perfect for breakfast, lunchboxes, after-school snacks, or even a healthier first birthday treat.
Anni Daulter originally created these muffins as a clever way to use leftover homemade baby purée, but they quickly became a family favorite. The fruit and vegetable purée keeps the muffins incredibly moist while adding natural sweetness and nutrients without relying on refined sugar.
Why You’ll Love These Mini Muffins
These spiced mini muffins are perfect for toddlers’ little hands and are packed with the same goodness they got when they were babies. These are also a great cupcake alternative for a one-year-old’s birthday party or as a mid-day snack.
- Freezer-friendly for easy meal prep
- Naturally sweetened with apples, squash, and raisins
- Made with whole wheat pastry flour
- Soft and tender for toddlers and kids
- Filled with cozy fall spices
- Great for breakfast, snacks, or lunchboxes
Ingredient Notes
A few quick notes before you begin:
Whole wheat pastry flour: Creates a soft, tender crumb while adding more fiber than all-purpose flour.
Apple, butternut squash & raisin purée: This homemade purée keeps the muffins moist while adding natural sweetness and nutrients.
Agave nectar: Adds a little extra sweetness. Maple syrup also works well if preferred.
Warm spices: Cinnamon, nutmeg, cloves, and allspice create a classic apple spice flavor that’s perfect for fall.
Apple, Butternut Squash & Raisin Purée
These muffins call for a homemade purée. The recipe originally came from Anni Daulter’s cookbook that shows parents how to save time by having their baby food purées do double duty for the family meals.
If you’re making them from scratch, here’s the quick version.
Ingredients
- 3 Fuji apples, peeled, cored, and chopped
- ½ butternut squash, peeled and cubed
- ¼ cup raisins
Instructions
Steam the apples and butternut squash together for 10–12 minutes, or until tender. Add the raisins during the last 2 minutes of cooking.
Transfer everything to a blender or food processor with about ½ cup of the reserved steaming liquid and blend until smooth, adding more liquid as needed to reach your desired consistency.
You’ll need 1½ cups of purée for this recipe.
If you have a baby, be sure to see our Apple, Butternut Squash & Raisin Baby Purée recipe for feeding tips, storage instructions, freezing guidance, and age recommendations.
How to Make Healthy Apple Spice Mini Muffins
Preheat the oven to 350°F. Line a mini muffin pan with paper liners or lightly grease each cup.
In a medium bowl, whisk together the whole wheat pastry flour, baking soda, cinnamon, nutmeg, cloves, allspice, and sea salt.
In a separate large bowl, beat the softened butter and maple syrup until light and creamy. Add the eggs one at a time, mixing well after each addition.
Stir in the apple, butternut squash, and raisin purée until fully combined.
Gradually add the dry ingredients, mixing just until no dry streaks remain. Avoid overmixing to keep the muffins light and tender.
Fill each muffin cup about three-quarters full.
Bake for 18–20 minutes, or until a toothpick inserted into the center comes out clean.
Let the muffins cool in the pan for about 5 minutes before transferring them to a wire rack.
Healthy Apple Spice Mini Muffins
Ingredients
- 2 cups 250 g whole wheat pastry flour
- 1 teaspoon 4.6 g baking soda
- 2 teaspoons 4.6 g cinnamon
- 1 teaspoon 2.2 g fresh nutmeg
- 1/4 teaspoon 0.5 g ground cloves
- 1/4 teaspoon 0.47 g allspice
- 1/2 teaspoon 3 g sea salt
- 1 cup 340 g pure maple syrup
- 1/2 cup 112 g unsalted butter, softened
- 3 eggs
- 1 1/2 cups Apple Squash, and Raisin Purée for Baby
- Fresh fruit and raisins for serving
Instructions
- Preheat the oven to 350°F (180°C).
- Combine all dry ingredients.
- In a separate bowl, using either a handheld or stand mixer on medium speed, beat butter with the agave nectar.
- Beat in the eggs, one at a time.
- Add in the purée.
- On low speed, add the flour mixture a little bit at a time until you have added it all and you have a cake-like batter.
- Line a mini muffin pan with cupcake liners and distribute batter equally, filling each about three-quarters full.
- Cook for 18 to 20 minutes, or until a toothpick inserted in the center comes out clean.
- Cool and serve warm with fresh fruit and raisins, if desired.
Nutrition
Frequently Asked Questions
Can I use store-bought baby food?
Yes. Unsweetened apple and squash baby food can be substituted if needed, though homemade purée provides the best flavor and texture.
Can I make regular-sized muffins?
Absolutely. Fill a standard muffin tin about two-thirds full and bake for approximately 20–25 minutes.
Can I make these dairy-free?
Yes. Substitute your favorite plant-based butter alternative with good baking results.
Can I freeze these muffins?
Yes. Once completely cooled, freeze for up to three months.
Are these muffins sweet?
They’re lightly sweet with a cozy apple spice flavor. Most of the sweetness comes naturally from the apples, squash, and raisins.
Hello, do you know if you can substitute the eggs with anything else…this sounds delicious but my son is allergic to eggs. Thank you in advance!
Kind regards,
Michelle
Great question! Flax meal can be used in place of eggs.
A tablespoon of flax meal in 3tbs of water.