Whole Wheat Rhubarb Applesauce Muffins

Finding a good use for early spring rhubarb can sometimes feel like a puzzle, especially when you’re not quite ready to commit to a full-blown pie or crumble. Plus, if you’re anything like me, you’re always on the hunt for breakfast or snack options that feel a little healthier without sacrificing flavor.

That’s where these rhubarb applesauce muffins come in handy. They’re moist and lightly spiced, they use applesauce to cut down on butter, and they’re a perfect way to use up that gorgeous rhubarb sitting in your fridge. Best of all, they’re easy enough to whip up on a Sunday afternoon for grab-and-go breakfasts all week long.

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What Kind of Rhubarb Should I Use?

Fresh rhubarb is always your best bet for these muffins, and you’ll find it in season during spring and early summer at most grocery stores and farmers markets. The color of the stalks – whether they’re bright red, pink, or even greenish – doesn’t really affect the flavor, so don’t worry if yours looks different than what you see in photos. Just make sure to trim off and discard the leaves, as they’re toxic, and only use the stalks. If fresh rhubarb isn’t available, frozen rhubarb works just fine too – no need to thaw it first, just chop it up and toss it right into your batter.

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Options for Substitutions

These muffins are pretty forgiving when it comes to swapping ingredients:

• Whole wheat flour: If you don’t have whole wheat flour, you can use all-purpose flour instead for a total of 3 cups. The muffins will be slightly lighter in texture and color.
• Rhubarb: Fresh rhubarb works best, but frozen rhubarb is totally fine – just thaw it first and drain any excess liquid. You can also substitute with chopped strawberries or a mix of both for a sweeter flavor.
• Applesauce: Use either sweetened or unsweetened applesauce depending on your preference. You could also try mashed bananas, though this will change the flavor profile a bit.
• Butter: You can swap butter with an equal amount of vegetable oil or melted coconut oil. If using oil, the muffins will be slightly more moist.
• Sugar: Feel free to reduce the sugar to 3/4 cup if you’re using sweetened applesauce, or try coconut sugar or brown sugar for a deeper flavor.
• Eggs: For each egg, you can use 1/4 cup additional applesauce or a flax egg (1 tablespoon ground flaxseed mixed with 3 tablespoons water, let sit for 5 minutes).

Watch Out for These Mistakes While Baking

The biggest mistake when making these muffins is overmixing the batter once you combine the wet and dry ingredients – stir just until everything is moistened, even if you see a few lumps, because overmixing develops the gluten and creates tough, dense muffins instead of light and tender ones.

Since rhubarb releases moisture as it bakes, cutting it into small, uniform pieces (about 1/2-inch) helps it distribute evenly and prevents soggy spots in your muffins.

Don’t skip greasing those muffin pans well, especially with the sugar content in this recipe, as the muffins can stick stubbornly to the pan – and if you’re using frozen rhubarb, don’t thaw it first or you’ll end up with extra liquid that throws off the batter consistency.

Finally, start checking for doneness at 18 minutes with a toothpick inserted in the center, as overbaking will dry out these muffins quickly.

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What to Serve With Rhubarb Applesauce Muffins?

These muffins are perfect for breakfast or brunch alongside a hot cup of coffee or tea. I love serving them warm with a pat of butter that melts right into all those nooks and crannies, or you can spread on some cream cheese for extra richness. They also make a great afternoon snack with a glass of cold milk, especially when the cinnamon sugar topping is still slightly crispy. If you’re putting together a brunch spread, set these out with fresh fruit, yogurt, and maybe some scrambled eggs to round out the meal.

Storage Instructions

Store: Keep your rhubarb applesauce muffins in an airtight container at room temperature for up to 3 days, or in the fridge for about a week. They stay moist really well thanks to all that applesauce, so they’re perfect for grabbing as a quick breakfast throughout the week.

Freeze: These muffins are great for freezing! Let them cool completely, then wrap each one individually in plastic wrap and store in a freezer bag for up to 3 months. It’s nice to have a stash ready for busy mornings.

Thaw: Just leave a frozen muffin on the counter for about 30 minutes to thaw, or pop it in the microwave for 20-30 seconds. If you want that fresh-baked feel, warm it in a 350°F oven for about 10 minutes after thawing.

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 2600-2900
• Protein: 30-36 g
• Fat: 65-75 g
• Carbohydrates: 510-550 g

Ingredients

For the muffin base:

• 2 1/4 cups flour (I always use King Arthur all-purpose flour for consistent results)
• 1 cup whole wheat flour
• 2 tsp baking powder
• 2 1/2 tsp cinnamon
• 1/4 tsp ground nutmeg
• 1/2 tsp baking soda
• 1/2 tsp salt
• 2 cups rhubarb (chopped into 1/2-inch pieces for even distribution)

For the wet mixture:

• 3/4 cup sugar
• 6 tablespoons butter (I like Kerrygold unsalted butter for this)
• 2 cups applesauce (I use Mott’s unsweetened for the best texture)
• 2 eggs (room temperature, about 70°F)

For the topping:

• cinnamon sugar

Step 1: Prepare Mise en Place and Preheat

• 2 cups rhubarb, chopped into 1/2-inch pieces

Preheat your oven to 400°F and grease two muffin pans (or line with muffin cups) to ensure they’re ready when your batter is prepared.

While the oven heats, chop the rhubarb into uniform 1/2-inch pieces—this consistent sizing ensures even cooking and distribution throughout the muffins.

Have all your ingredients measured and ready to go, as the mixing process moves quickly once you begin.

Step 2: Mix Dry Ingredients with Rhubarb

• 2 1/4 cups flour
• 1 cup whole wheat flour
• 2 tsp baking powder
• 2 1/2 tsp cinnamon
• 1/4 tsp ground nutmeg
• 1/2 tsp baking soda
• 1/2 tsp salt
• 2 cups rhubarb, chopped into 1/2-inch pieces

In a large mixing bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, cinnamon, nutmeg, baking soda, and salt until evenly combined.

Add the chopped rhubarb and gently fold it in to coat the pieces with flour—this helps prevent the rhubarb from sinking to the bottom of the muffins during baking.

I like to use King Arthur all-purpose flour because it gives consistent, reliable results every time.

Step 3: Create the Wet Ingredient Base

• 6 tablespoons butter
• 3/4 cup sugar
• 2 cups applesauce
• 2 eggs

In a second bowl, melt the butter and then add the sugar, stirring until combined.

Whisk in the applesauce and eggs, stirring until the mixture is smooth and well-blended.

Make sure the eggs are incorporated thoroughly so they distribute evenly through the batter—this ensures consistent texture across all your muffins.

I always use Mott’s unsweetened applesauce because it has the perfect texture and won’t make the batter too thin.

Step 4: Combine Wet and Dry Ingredients

• dry ingredient mixture from Step 2
• wet ingredient mixture from Step 3

Pour the wet ingredient mixture from Step 3 into the dry ingredient mixture from Step 2, and gently stir until just combined—the batter should be lumpy and slightly streaky.

Don’t overmix, as this can develop the gluten and result in tough, dense muffins.

A few flour streaks are perfectly fine and actually desirable for tender muffins.

Step 5: Fill and Top Muffin Cups

• batter from Step 4
• cinnamon sugar

Divide the batter evenly among 18 muffin cups, filling each about 2/3 full—this leaves room for the muffins to rise without overflowing.

Sprinkle a pinch of cinnamon sugar on top of each muffin for a sweet, cinnamon-flavored crust that adds texture and visual appeal.

Step 6: Bake Until Golden

Place the muffin pans in your preheated 400°F oven and bake for 18 to 20 minutes, until the muffins are golden brown on top and a toothpick inserted into the center comes out clean or with just a few moist crumbs.

Allow the muffins to cool in the pan for 5 minutes before turning them out onto a wire rack, which prevents them from becoming soggy on the bottom.

Whole Wheat Rhubarb Applesauce Muffins

Delicious Whole Wheat Rhubarb Applesauce Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 30 minutes mins

Total Time 47 minutes mins

Servings 18 muffins

Calories 2750 kcal

Ingredients

  

For the muffin base::

• 2 1/4 cups flour (I always use King Arthur all-purpose flour for consistent results)
• 1 cup whole wheat flour
• 2 tsp baking powder
• 2 1/2 tsp cinnamon
• 1/4 tsp ground nutmeg
• 1/2 tsp baking soda
• 1/2 tsp salt
• 2 cups rhubarb (chopped into 1/2-inch pieces for even distribution)

For the wet mixture::

• 3/4 cup sugar
• 6 tablespoons butter (I like Kerrygold unsalted butter for this)
• 2 cups applesauce (I use Mott's unsweetened for the best texture)
• 2 eggs (room temperature, about 70°F)

For the topping::

• cinnamon sugar

Instructions

 

• Preheat your oven to 400°F and grease two muffin pans (or line with muffin cups) to ensure they're ready when your batter is prepared. While the oven heats, chop the rhubarb into uniform 1/2-inch pieces—this consistent sizing ensures even cooking and distribution throughout the muffins. Have all your ingredients measured and ready to go, as the mixing process moves quickly once you begin.
• In a large mixing bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, cinnamon, nutmeg, baking soda, and salt until evenly combined. Add the chopped rhubarb and gently fold it in to coat the pieces with flour—this helps prevent the rhubarb from sinking to the bottom of the muffins during baking. I like to use King Arthur all-purpose flour because it gives consistent, reliable results every time.
• In a second bowl, melt the butter and then add the sugar, stirring until combined. Whisk in the applesauce and eggs, stirring until the mixture is smooth and well-blended. Make sure the eggs are incorporated thoroughly so they distribute evenly through the batter—this ensures consistent texture across all your muffins. I always use Mott's unsweetened applesauce because it has the perfect texture and won't make the batter too thin.
• Pour the wet ingredient mixture from Step 3 into the dry ingredient mixture from Step 2, and gently stir until just combined—the batter should be lumpy and slightly streaky. Don't overmix, as this can develop the gluten and result in tough, dense muffins. A few flour streaks are perfectly fine and actually desirable for tender muffins.
• Divide the batter evenly among 18 muffin cups, filling each about 2/3 full—this leaves room for the muffins to rise without overflowing. Sprinkle a pinch of cinnamon sugar on top of each muffin for a sweet, cinnamon-flavored crust that adds texture and visual appeal.
• Place the muffin pans in your preheated 400°F oven and bake for 18 to 20 minutes, until the muffins are golden brown on top and a toothpick inserted into the center comes out clean or with just a few moist crumbs. Allow the muffins to cool in the pan for 5 minutes before turning them out onto a wire rack, which prevents them from becoming soggy on the bottom.