Whole wheat rhubarb muffins are delicious hearty muffins made with fresh rhubarb. With just a few simple ingredients, you can whip up these wholesome muffins for an easy grab-and-go breakfast.

Brown sugar, flour and ground flaxseed are mixed together and then combined with yogurt, eggs, oil and chopped tart rhubarb to create the muffin batter. Perfect for busy mornings or healthy snack served with coffee, tea, spiced latte or one of our healthy homemade smoothie recipes.

Close up of a few rhubarb muffins on a table with pink cupcake liners.

Easy Fluffy Muffins

Rhubarb is a wonderful vegetable (no it’s not actually a fruit) to use in baking recipes. It has a tart flavor that lends perfectly to the sweetness like strawberries in our rhubarb crisp. Today’s recipe uses just rhubarb, but berries can also be added if desired.

These muffins are easy with just a few simple ingredients from the grocery store.
A combination of whole wheat flour, all-purpose flour, and ground flaxseed add loads of healthy fiber.
These are so easy to make, just add dry ingredients to wet ingredients and fold in chopped rhubarb.
These muffins can be stored in the fridge for up to 1 week, and freeze beautifully for future breakfasts, brunches and snacks.

Serve these muffins with butter, yogurt, whipped coconut cream, or alongside a raspberry smoothie.

Recipe ingredients on table including bowls of yogurt, flours, brown sugar, eggs and sticks of rhubarb.

Recipe Ingredient List

RHUBARB: Rhubarb season is the perfect time to buy this affordable vegetable for baking recipes. Grab a bundle from the local farmer’s market or neighbor’s back yard and chop it into small pieces. Add some to this recipe and freeze the rest for future baking.

DRY INGREDIENTS: Whole wheat flour, all-purpose flour and ground flaxseed are combined with brown sugar, baking soda and salt. This variety of flours adds more healthy fiber to these muffins.

WET INGREDIENTS: Plain yogurt, eggs, vegetable oil and vanilla extract are mixed with the dry ingredients to create a batter.

VARIATIONS: Replace flours with whole wheat pastry flour. Yogurt can be replaced with 1 cup milk or 1 cup buttermilk. Try whole oats instead of ground flaxseed. Add in sunflower seeds or pumpkin seeds. For a heartier muffin, replace whole-wheat flour with whole spelt flour.

Four images showing steps to make recipe including mixing bowls with unmixed ingredients and a spoon, uncooked muffins in paper liners in muffin pan, and baked muffins on a wire rack.

How To Make Healthy Rhubarb Muffins

Freshly baked rhubarb muffins taste perfect when served fresh out of the oven!

Chop the rhubarb into small, bite-size pieces. The smaller the better. No need to remove the skin.
Mix whole grain flour, all purpose flour, flaxseed, baking soda and salt in a large bowl according to the full instructions in the recipe card below.
Mix yogurt, eggs, vanilla extract, and oil in a separate bowl. Make a well in the center of dry ingredients and pour it inside. Gently stir together until a batter is formed.
Fold in the chopped rhubarb to batter. Add to a muffin tin with liners. Bake and enjoy warm!

Leftover rhubarb muffins can be stored in an airtight container on the counter or in the fridge for up to 3-4 days.

These muffins freeze beautifully. I prefer to wrap each one in parchment (or use plastic wrap) and add them to a freezer bag. Remove as much air as possible and seal tightly. These will keep fresh up to 6 months.

These can be popped straight in the microwave while still frozen. Remove parchment and wrap in a paper towel. Microwave for about 30 seconds and serve.

One rhubarb muffin sliced in half with more muffins and rhubarb sticks in background.

Recipe Tips

Chop the rhubarb into small pieces with a sharp knife. The smaller the better. No need to remove the fibrous skin.
Mix rhubarb well into batter so that it’s not clumped together. Clumped rhubarb won’t bake as well in the muffin batter. Freeze any leftover chopped rhubarb for future recipes.
Use an ice cream or cookie scoop to drop the batter into the muffin pan. If you don’t have one a spoon will work too. Fill each cup about 3/4 full. Use paper muffin cups for easy clean-up.
Bake until a toothpick comes out clean, about 18-20 minutes. Tops of muffins will be a light golden brown.
Make a double batch of these muffins and store the rest in the freezer!
If rhubarb is too tart for you, consider reducing the rhubarb by half and adding fresh chopped strawberries to the batter.

Rhubarb muffins close up with sticks of rhubarb in the background.

More Muffin Recipes

Lemon Blueberry Muffins are high in fiber and full of sweet and zesty lemon flavor.
Applesauce Oatmeal Muffins are a wholesome breakfast recipe.
Whole Wheat Buttermilk Streusel Muffins are hearty and delicious.
Cottage Cheese Muffins are light and sweet tasting.
Baked Oatmeal Cups are one of our popular recipes with 6 easy flavor additions.

Whole Wheat Rhubarb Muffin Recipe

Delicious hearty muffins made with fresh rhubarb.

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Prep Time: 12

Cook Time: 20

Total Time: 32

Servings: 18 muffins

Ingredients

1 cup whole wheat flour
1 cup all purpose flour
½ cup ground flaxseed - or wheat germ
½ cup dark brown sugar - honey, maple syrup or coconut sugar
1 tsp baking soda
¼ tsp salt
1 cup plain yogurt - or greek yogurt
2 eggs - beaten
3 Tbsp vegetable oil - or coconut oil
½ tsp vanilla extract
2 cups chopped rhubarb - fresh or thawed

Instructions

Preheat the oven to 375°F. Chop the rhubarb into small pieces.
Add dry ingredients to a large bowl: whole wheat flour, all purpose flour, ground flaxseed, brown sugar, baking soda and salt. Mix together.
Add wet ingredients to a medium bowl: yogurt, beaten eggs, vegetable oil and vanilla extract. Mix together.
Make a well in the center of the dry ingredients, then pour the wet ingredients into the center. Fold the dry ingredients into the middle until muffin batter is evenly mixed.
Fold the chopped rhubarb into the muffin batter just until combined. Do not overmix.
Place paper liners into a muffin pan. Fill each muffin cup ¾ full. Bake for 18-22 minutes, or until tops are golden and a toothpick comes out clean when poked through the center.
Let cool 5 minutes, then transfer to a wire rack to cool completely. Serve and enjoy!

Recipe Notes:

Leftover rhubarb muffins can be stored in an airtight container on the counter or in the fridge for up to 3-4 days.
These muffins freeze beautifully. I prefer to wrap each one in parchment (or use plastic wrap) and add them to a freezer bag. Remove as much air as possible and seal tightly. These will keep fresh up to 6 months.
VARIATIONS: If rhubarb is too tart for you, consider reducing the rhubarb by half and adding fresh chopped strawberries to the batter.
Replace flours with whole wheat pastry flour. Yogurt can be replaced with 1 cup milk or 1 cup buttermilk. Try whole oats instead of ground flaxseed. Add in sunflower seeds or pumpkin seeds. For a heartier muffin, replace whole-wheat flour with whole spelt flour.
Chop the rhubarb into small pieces with a sharp knife. The smaller the better. No need to remove the fibrous skin.
Mix rhubarb well into batter so that it’s not clumped together. Clumped rhubarb won’t bake as well in the muffin batter. Freeze any leftover chopped rhubarb for future recipes.
Use an ice cream or cookie scoop to drop the batter into the muffin pan. If you don’t have one a spoon will work too. Fill each cup about 3/4 full. Use paper muffin cups for easy clean-up.

Nutrition

The nutritional information provided is an estimate and is per serving.

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Whole Wheat Rhubarb Muffins