Easy Applesauce Muffins (Whole Wheat and Chia)
These healthy applesauce muffins are light, fluffy and packed with chia seeds, whole wheat pastry flour and warm cinnamon. They’re sweetened with honey or pure maple syrup, with no butter and no eggs.
They’re a quick solution to breakfast and will give you all the energy you need to keep up with your summer activities. Approved by my husband, my 3 year old and my baby!

The Best Easy Applesauce Muffins (Whole Wheat and Chia)
I cannot believe we’re on the last half of July! Does anyone else feel like this year is flying by? I want to slam the brakes on my summer days, especially since my baby boy is rapidly approaching his first birthday! I tear up thinking about it. Am I the only mom who gets emotional on birthdays? If so… just lie and say you get me. At this point, all I can do is hang on, enjoy every second, and comfort myself with these light, fluffy applesauce muffins. My cute baby smeared his muffin all over his face while he hastily ate it.

Before I started blogging, I was clueless on how this all worked. It is hard work juggling everything! I quickly realized this blogging business is packed with talented, educated and family focused individuals who spend long, late hours working while our kiddos sleep. Although I love creating healthy recipes and hosting my health challenge, I wanted to do more, so I united with my brilliant friend, Sabrina, to host a food blogger conference unlike any out there.
I now have 4 babies: my two beautiful children, No Diets Allowed and Everything Food Conference. My two kids are by far the most rewarding, and they keep me motivated to tweak recipes until I reach perfection. Watching them inhale these chia seed applesauce muffins makes me smile. If their tummies are happy and healthy, this mama is happy.

Why You’ll Love These Healthy Applesauce Muffins
- Light and fluffy. Whole wheat pastry flour and a gentle stir keep them tender, not dense.
- No eggs or butter. Applesauce and olive oil keep them moist without either one.
- Naturally sweetened. Honey or pure maple syrup does all the sweetening, with no refined sugar.
- Kid approved. A wholesome grab and go breakfast or snack for the whole family, from toddlers to grown ups.
Ingredients You’ll Need
Here is what goes into these chia seed applesauce muffins and why each one matters. Exact amounts are in the recipe card below.
- Whole wheat pastry flour: Finer and softer than regular whole wheat flour. It is milled from soft wheat with less protein, so it forms less gluten and keeps these muffins light and fluffy. I rant and rave over Bob’s Red Mill whole wheat pastry flour, and I was giddy when this favorite brand sponsored Everything Food Conference.
- Chia seeds: These tiny seeds add fiber, a little crunch and nutrition. They also soak up some of the liquid in the batter, which helps hold the muffins together. I love Bob’s Red Mill chia seeds too.
- Baking powder and baking soda: Both give the muffins lift. Aluminum free baking powder avoids any metallic aftertaste, and the baking soda reacts with the acidic applesauce for a soft, domed top.
- Cinnamon: Adds warmth and brings out the apple flavor. Make sure yours is fresh and fragrant, since old ground cinnamon loses its punch.
- Applesauce: Replaces the butter and eggs, adding moisture and natural sweetness. Unsweetened applesauce lets the honey or maple syrup control the sweetness.
- Honey or pure maple syrup: Use either one. Maple syrup keeps the muffins free of animal products, and honey gives a warm, floral note.
- Olive oil: Keeps the crumb moist. Oil stays liquid at room temperature, so oil based muffins stay soft even after they cool. A light olive oil keeps the flavor mild.
- Milk of your choice: Any milk works. Vanilla almond milk adds a subtle vanilla note and keeps the muffins dairy free. Cow’s milk, oat milk or soy milk all work.
- Pure vanilla extract: Rounds out the cinnamon and apple flavors and makes the muffins taste bakery sweet.

How to Make Applesauce Chia Muffins
- Heat the oven. Preheat to 375°F and grease a muffin tin, or line it with paper liners. A fully heated oven gives the muffins a quick burst of rise and nicely rounded tops.
- Mix the dry ingredients. In a medium bowl, combine the flour, chia seeds, baking powder, baking soda and cinnamon. Whisk well so the leaveners and chia are spread evenly and you don’t end up with bitter pockets of baking soda.
- Mix the wet ingredients. In a small bowl, stir together the applesauce, honey or maple syrup, olive oil, milk and vanilla until smooth. Stir well so the oil and honey blend completely into the applesauce.
- Combine. Pour the wet ingredients into the dry and stir just until the batter is moist. A few lumps are fine. Overmixing whole wheat batter makes muffins tough.
- Fill the tin. Pour 1/4 cup of batter into each muffin cup so they all bake evenly. A measuring cup or large cookie scoop makes this quick and tidy.
- Bake. Bake for 20 to 22 minutes, until the tops are golden brown, spring back when lightly pressed and a toothpick inserted in the center comes out clean.
- Cool. Let them cool in the tin for a few minutes, then move them to a wire rack so the bottoms don’t get soggy.
Kami’s tip: Stir the wet ingredients into the dry just until the batter is moist. Stopping early is what keeps these muffins light and fluffy.

Ways to Customize Applesauce Muffins
- Add fruit. Fold in diced fresh apple or a handful of blueberries just before scooping.
- Add crunch. Stir in chopped walnuts or pecans, or sprinkle a few on top before baking.
- Spice it up. Add a pinch of nutmeg or ginger along with the cinnamon.
- Raisins. Mix in raisins or dried cranberries for little bursts of sweetness.
Applesauce Muffins FAQs
- Are these muffins dairy free? Yes, as long as you use a nondairy milk like almond milk.
- Are they vegan? Use pure maple syrup instead of honey and a plant based milk, and they are free of animal products.
- Do I need to soak the chia seeds first? No. They go right into the dry ingredients and soak up liquid as the batter sits and bakes.
- Can I use regular whole wheat flour? You can, but the muffins will be denser. Whole wheat pastry flour is what makes them light and fluffy.
- Can I use homemade applesauce? Yes. Smooth homemade applesauce works great. If it is very chunky, mash or blend it first so the batter stays even.
- Can I use sweetened applesauce? Yes, but the muffins will be sweeter. You can cut back slightly on the honey or maple syrup.
- How do I know when they’re done? The tops will be golden brown and a toothpick in the center will come out clean, after 20 to 22 minutes.
- Can I make mini muffins? Yes. Fill a greased mini muffin tin and start checking them early, since smaller muffins bake faster.
- How do I store them? Keep cooled muffins in an airtight container at room temperature for up to 2 days, or refrigerate for longer.
- Can I freeze applesauce muffins? Yes. Freeze them in a freezer bag for up to 3 months and thaw at room temperature or warm briefly in the microwave.
Kitchen Tools for This Recipe

Chia Seed Applesauce Muffins
Ingredients
- 2 cups whole wheat pastry flour
- 1/4 cup organic chia seeds
- 2 teaspoons aluminum-free baking powder
- 1/2 teaspoon baking soda
- 1 teaspoon cinnamon
- 1 cup applesauce
- 1/2 cup honey or pure maple syrup
- 1/2 cup olive oil
- 1/4 cup milk of your choice... I used vanilla almond milk
- 2 tsp pure vanilla extract
Instructions
- Preheat oven to 375.
- In a medium-sized bowl, combine flour, chia seeds, baking powder, baking soda, and cinnamon.
- In a small bowl, combine applesauce, honey, oil, milk, and vanilla. Stir well. Pour into dry ingredients and stir just until batter is moist.
- In a greased muffin tin, pour 1/4 cup batter into each tin.
- Bake for 20 to 22 minutes until golden brown and toothpick comes out clean.
Made these muffins? Leave a star rating in the recipe card and tell me how they turned out in the comments below. I love hearing how your family enjoys them and which mix ins you tried.
More Recipes You’ll Love
- Healthy Cranberry Orange Muffins
- Pumpkin Banana Muffins
- Banana Zucchini Muffins
- Blueberry Banana Muffins
- Eggless Muffins
Want more lighter bakes? Browse the Healthy Muffin Recipes on our sister site, Everything Muffins.
