These Healthier Apple Rhubarb Muffins are one of my favorite ways to use that abundant garden rhubarb! You can make them in the spring or summer when rhubarb is in season, or chop and freeze it to make all year! With healthier ingredient swaps like almond flour, yogurt, and maple syrup instead of sugar, that delicious streusel topping makes these a family favorite!

- From the Spring Garden - I've never grown my own rhubarb, but a neighbor always has plenty to share! Apples are available all year so they are an easy healthy addition to these yummy muffins!
- Healthier Ingredients - Usually rhubarb recipes are loaded with sugar, but these muffins are lightened up with a bit of real maple syrup, along with the natural sweetness from the apple. If you've got rhubarb, try some in my Mixed Berry Rhubarb Crisp and this Strawberry Rhubarb Sauce!
- Extra Protein - With 4g of protein in each muffin, almond flour, oats, egg and yogurt make these muffins nutrient dense and a great snack that feels like a treat!
- If you Love Healthier Muffins, try my Strawberry Rhubarb Muffins and these Double Chocolate Zucchini Muffins! If you love healthier baking, you might also love my ebook, The Healthier Baking Cookbook!
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Ingredients & Substitutions
With real fruits and vegetables, oats, almond flour and yogurt, these healthy muffins are great to have a batch on the counter to reach for, even with the kids who claim they dislike rhubarb!

- Flour, Almond Flour & Oats - A healthier mix of all-purpose flour, almond flour, and regular rolled oats add protein. You can substitute any type of flour, including gluten-free flour, and use oats labeled regular rolled, old fashioned, thick rolled, or quick oats. I like to get oats from the bulk bin at the grocery store.
- Maple Syrup - Tart rhubarb usually means a ton of white sugar! I like to use real maple syrup instead for a sweet treat that isn't too overly sweet, with a little brown sugar in the topping. Try making your own Homemade Brown Sugar next time you run out!
- Yogurt - Keeps the muffins moist and adds protein!
- Apples and Rhubarb - Use fresh rhubarb or frozen chopped rhubarb, and 2 cups chopped of any apple variety. This could be 2 apples or possibly less, depending on their size.
- Streusel Topping - Almond flour, brown sugar, oats and butter make up that delicious topping that makes everyone reach for a second muffin!
See recipe card for quantities.
Instructions
Chop, mix, and bake, these muffins are made in 1 bowl and prepped in about 10 minutes!

Step 1 - Preheat the oven to 375°F. Chop and measure the rhubarb and apples.

Step 2 - Mix the dry ingredients in a bowl.

Step 3 - Add everything else and mix until just combined.

Step 4 - Evenly distribute the batter between 12 paper lined muffin cups. Mix up the streusel topping in a small bowl and sprinkle over each muffin.
Bake about 25 to 30 minutes.
Do not open the oven to peek or check for at least 25 minutes! Allow to cool and serve with butter.
Recipe Notes & Helpful Tips
- Don't Open the Oven to Peek! - This is often the biggest mistake with muffins! Muffins need a consistent hot heat to rise. Opening the oven door causes a temperature drop which can cause the muffins to sink in the middle. Preheat the oven, set a timer, and let the muffins bake uninterrupted for at least 25 minutes before checking.
- Let them Cool - Muffins hot from the oven are still carry-over cooking. Let them sit on the stovetop to firm up and cool.
- Fill the cups generously - Healthier muffins don't rise as dramatically as a refined sugar muffin, so filling the cups almost full gives you a nice rounded top with plenty of streusel.
- Storage and Freezing - Muffins can be stored in an airtight container on the counter for a couple days, or in the fridge for about 4 or 5 days. They can be frozen for up to 4 months.

Recipe FAQs
Muffins can sink in the middle when the oven door is opened during baking or if they are not baked long enough and the middle is not done. Muffins need a consistent hot temperature to rise. Opening the door and checking on them too early or too often can cause the uncooked center to sink. Set a timer and don't open the oven for at least 25 minutes. If your centers sink a little or don't dome up, that's ok, they are still delicious!
Yes, fresh or frozen rhubarb will work for this recipe. Rhubarb can be washed and chopped and frozen flat in freezer bags. Add it frozen to the batter, breaking up any clumps.
The almond flour adds nutrition and protein, but if you have a nut allergy or just don't it, you can use a mixture of more all purpose flour and oats. Or you can substitute any other nut or oat flour, or use gluten-free flour.
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Apple Rhubarb Muffins
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Print Pin RateIngredients
- ½ cup flour
- ½ cup almond flour
- 1 cup oats
- 1 teaspoon baking soda
- 1 teaspoon baking powder
- ½ teapoon kosher salt
- ⅓ cup plain yogurt
- ⅓ cup maple syrup
- 2 Tablespoons butter melted
- 2 teaspoons vanilla extract
- 1 egg
- 2 cups apples chopped (about 2 or less apples)
- 1 cup rhubarb chopped (2 to 3 stalks)
For the Streusel Topping
- 3 Tablespoons brown sugar
- 3 Tablespoons almond flour
- 3 Tablespoons oats
- 1 Tablespoon butter melted
Instructions
- Preheat the oven to 375℉.
- Add all dry ingredients to a bowl and mix.
- Chop and measure the rhubarb and apples (no need to peel). Add all ingredients to the bowl and mix.
- Add the batter evenly to 12 paper lined muffin cups, filled full.
- Mix together the streusel topping and sprinkle over each muffin.
- Bake for 25 to 30 minutes without opening the oven door or peeking! Allow to cool and enjoy with butter!
Notes
- Chop apples and rhubarb small.
- Don't open the oven door or peek while the muffins are baking.
- Check for doneness after 25 or 30 minutes and bake 5 extra minutes if not done.










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