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These Healthy Rhubarb Apple Muffins are moist, fluffy, lightly sweetened and make a perfect healthy snack or breakfast. Naturally sweetened with applesauce and maple syrup, these muffins are full of whole grains, fiber and protein, with the sweet and tangy flavor of rhubarb.

Healthy Apple Rhubarb Muffin split in half with a pat of melting butter on it.

Is there another more quintessential spring ingredient than rhubarb? When I was growing up in Alaska, I remember all of my friends parents had rhubarb growing in their gardens. As a child it is hard to like rhubarb unless it is wrapped up in a dessert like Old Fashioned Rhubarb Crumble or Strawberry Rhubarb Crisp. On its own, rhubarb is very tart. But when combined with another fruit and a little sweetness, it has a fresh and juicy flavor that you can’t get anywhere else.

Healthy Apple Rhubarb muffin batter

These Healthy Apple Rhubarb Muffins are based on my Healthy Apple Muffin recipe. The grated apple and applesauce lend their natural sweetness to the tart rhubarb. I used whole wheat pastry flour here, which has the same nutritional value as regular whole wheat flour but leads to a lighter, fluffier muffin. I also tossed the chopped rhubarb in some flour before mixing it with the batter to keep it all from sinking to the bottom of the muffin while cooking.

Apple Rhubarb muffin batter

What are the ingredients for Healthy Apple Muffins?

  • Chopped Rhubarb – Remove any of the dark green leaves as those are toxic. Chop into a small dice so that the rhubarb mixes well into the batter.
  • Grated Apple – adds sweetness, moisture, and lots of apple flavor!
  • Unsweetened Apple Sauce – adds more apple flavor, moisture and natural sweetness.
  • Pure Maple Syrup – adds a touch of sweetness without using refined sugar.
  • Butter – adds flavor and moisture. You can use vegan butter for dairy free
  • Eggs – for moisture and binding
  • Milk – you can use dairy milk or non dairy milk
  • Apple Cider Vinegar – the secret ingredient! This is what makes them so tender and fluffy. It does NOT make them taste like vinegar at all.
  • Pure Vanilla Extract – more flavor!
  • Whole Wheat Pastry Flour – using whole wheat pastry flour is what makes these super light and fluffy with the nutritional benefits of whole wheat flour.
  • Cinnamon – the subtle spice just makes these more delicious.
  • Baking Soda – makes the muffins rise.
  • Baking Powder – This is different than baking SODA and yes, you need both of them.
  • Salt – don’t skip it! Without salt, these muffins will be bland.
Rhubarb apple muffin batter in a muffin tin before baking

Tips for making the best Rhubarb Apple Muffins

It’s important to mix the wet and dry ingredients in two different bowls. Mix them very well. After combining the wet ingredients with they dry ingredients, you want to just mix them until they come together. Do this by hand and don’t use a mixer. If you over mix the batter, the muffins will be tough.

Be sure to chop the rhubarb into pieces no larger than 1/2 inch. Before mixing the rhubarb into the muffin batter, toss it with 1 tablespoon of flour. This helps the rhubarb to stay evenly distributed throughout the muffin instead of sinking to the bottom.

Another trick I like to use for making muffins fluffy is using a little bit of vinegar. Why does vinegar make muffins fluffy? It increases the acidity of the batter and reacts with the baking soda to create a better rise. It is similar to using buttermilk or yogurt in a recipe, like in my blueberry buttermilk pancakes.

Apple Rhubarb muffins on a wire rack

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Healthy Apple Rhubarb Muffins

Servings 12 Muffins
These Healthy Rhubarb Apple Muffins start with a blast of heat for the first 5 minutes, then the heat is turned down for the remainder of the baking tie. This allows them to puff up and get extra tall and fluffy!


Wet Ingredients

  • ¼ cup unsalted butter Melted. Can use vegan butter or dairy butter.
  • 3/4 cup unsweetened apple sauce
  • 1/2 cup pure maple syrup
  • 1 cup apple grated, with or without peel.
  • 1 cup rhubarb chopped to 1/2 inch dice
  • 2 eggs beaten
  • ¼ cup milk can use dairy milk or dairy free milk
  • 1 teaspoon apple cider vinegar
  • 1 teaspoon pure vanilla extract

Dry Ingredients

  • 2 cups whole wheat pastry flour 289 grams – plus one table spoon set aside for tossing with rhubarb
  • 1.5 tsp cinnamon 4 grams
  • 1 tsp baking soda 6 grams
  • 1 tsp baking powder 6 grams
  • 1/4 teaspoon fine sea salt 2 grams


  • Preheat oven to 425 degrees. Line a muffin tin with muffin liners or spray with cooking spray, set aside.
  • In one bowl, combine the dry ingredients, whisk until combined.
  • In a second bowl, mix together the wet ingredients, except for the chopped rhubarb. Mix until fully combined.
  • Pour the dry ingredients into the wet ingredients and use a spatula to mix them until just combined. Do not over mix.
  • Before adding the rhubarb to the muffin batter, toss it with a tablespoon of flour until every pieces is coated. Then fold the rhubarb into the batter until just combined and no dry spots remain. Do not over mix or muffins will be tough.
  • Evenly distribute the batter into the muffin tins. Each muffin cup will be nearly full. I like to use an ice cream scoop for easy portioning.
  • Place muffins in the oven and bake for 5 minutes. Without taking the muffins out of the oven, turn the heat down to 350 degrees F. Bake for another 17 minutes, or until a toothpick inserted into the center of a muffin comes out clean.
  • Remove muffins from oven and as soon as they are cool enough to handle, remove them from the muffin pan and allow to cool completely on a wire cooling rack.


Muffins freeze very well.  Allow to cool completely and then move to a freezer bag.  Freeze for up to 3 months.  Muffins can be thawed at room temperature or in the microwave for 30-60 seconds. 


Serving: 1Muffin | Calories: 167kcal | Carbohydrates: 28g | Protein: 4g | Fat: 5g | Saturated Fat: 3g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 1g | Trans Fat: 0.2g | Cholesterol: 38mg | Sodium: 220mg | Potassium: 175mg | Fiber: 3g | Sugar: 11g | Vitamin A: 189IU | Vitamin C: 1mg | Calcium: 65mg | Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Additional Info

Did you like this recipe?Please comment, rate and share! And don’t forget to tag me on Instagram @foxandbriar AND #foxandbriar so I can see what you made!
Hello! I’m Meghan.

I am so glad that you are here! I am the recipe developer, photographer, and writer here at my blog Fox and Briar. I am a passionate, self-taught home cook and believe that most things are better homemade and that good food doesn’t need to be complicated.

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