Healthy Gluten Free Oat Rhubarb Muffins with Streusel

These rhubarb gluten free muffins are the easy kind of baking we all need. Tart rhubarb, almond + oat flours, and a quick oat streusel on top. They’re lightly sweet, soft in the middle, crunchy on the top—basically healthy rhubarb muffins that taste like a bakery treat! If you’re after oat rhubarb muffins with real fiber and big flavor, this delicious muffin recipe is the one to save!

Healthy Gluten Free Oat Rhubarb Muffins with Streusel

In early spring, when I see stalks of rhubarb beginning to sprout, I get so excited to make all kinds of delicious things with those tart stalks.

I love saving and freezing rhubarb, then pairing it with fresh strawberries to make low sugar strawberry rhubarb jam.

Rhubarb is such a unique vegetable to add to baked goods. We love it in these muffins!

The sweetness from the oatmeal streusel pairs perfectly with the tartness.

These gluten-free muffins are easy to make and are a fabulous addition to lunchboxes or your next breakfast spread.

Why you’ll love this rhubarb streusel muffins recipe

Naturally gluten-free – Made with oat flour, almond flour, and coconut flours—my favorite combo for gluten-free baking, plus no xanthan gum is needed!

Easy to make – If I can make a muffin batter in one bowl, you better believe I’m going to! The streusal mixes easily too, making this a minimal-dish recipe.

Meal prep + freezer-friendly – Bake once, and enjoy for healthy snacks all week! They freeze great, too.

Ingredients you’ll need for gluten free rhubarb muffins

Scroll down to view the recipe card below for the full ingredients list, nutrition facts, and step-by-step instructions.

• Eggs – Use large eggs, ideally at room temperature so the batter mixes evenly and rises well.
• Unsweetened almond milk – Any milk works (oat, cashew, dairy). If using sweetened milk, reduce the sugar by 1–2 tablespoons.
• Unsweetened applesauce – Adds moisture and a little natural sweetness so we can use less oil. If using sweetened applesauce, reduce the sugar slightly.
• Avocado oil – Neutral flavor and helps a tender crumb. Melted coconut oil or light olive oil are fine swaps.
• Vanilla extract – Rounds out the rhubarb’s tartness. Optional but lovely: 1–2 tsp lemon zest or orange zest for a bright bakery vibe.

• Oat flour – Soft, wholesome base that keeps these tender. Use certified gluten-free to ensure it’s totally gluten-free.
• Almond flour – Choose finely ground blanched almond flour (not almond meal) for moisture and richness.
• Coconut flour – Super absorbent; measure carefully. Don’t substitute 1:1 with other flours.
• Natural cane sugar – Just enough sweetness to balance tart rhubarb. You can use coconut sugar or light brown sugar for a deeper flavor.
• Baking powder
• Sea salt
• Fresh rhubarb, diced small – Cut into ¼-inch pieces so they bake through. If using frozen, keep pieces small, don’t thaw, and toss with 1 tsp oat flour before folding in to prevent excess moisture.

Streusel Ingredients

• Coconut oil – Slightly softened so the streusel clumps. Butter or ghee also work.
• Rolled oats – Old-fashioned oats give great crunch. Quick oats make a finer crumb.
• Oat flour  – Helps the topping hold together (grind rolled oats if you’re out).
• Cinnamon – Warm spice that pairs beautifully with rhubarb; add a pinch of cardamom or nutmeg if you like.
• Natural cane sugar – Sweet, crisp finish. Brown sugar or coconut sugar add a caramel note.

How to make healthy rhubarb muffins

Step 1: Preheat the oven to 350 degrees F. Line a 12-cup muffin tin with paper or silicone liners.

Step 2:  In a large bowl whisk eggs, almond milk, applesauce, avocado oil, and vanilla until smooth. 

Step 3: Sprinkle in oat flour, almond flour, coconut flour, sugar, baking powder, and salt. Stir the dry ingredients just until no dry pockets remain. Fold in diced rhubarb.

Step 4: Divide the muffin batter among 12 cups (a level ice-cream scoop works well).

Step 5: In a small bowl, mash coconut oil with oats, oat flour, cinnamon, and sugar until crumbles form. Scatter evenly over the batter.

Step 6: Bake 22–24 minutes, until tops are set and edges are light golden. A toothpick should come out slightly moist—not wet, not bone dry. Let muffins rest 5 minutes in the pan, then move to a wire rack to cool.

Watch me make rhubarb muffins gluten-free

The full how to video can be watched below, or on my YouTube channel!

How to store

Store leftovers muffns in an airtight container at room temperature for 1–2 days, or refrigerate up to 5 days. Be sure to allow the muffins to fully cool before adding to

To freeze, wrap muffins individually and freeze up to 3 months. Thaw overnight in the fridge or reheat from frozen at 300°F for 10–12 minutes.

Substitutions, optional variations & dietary adjustments

Below you’ll find a list of substitutions that will work well in this gluten-free rhubarb muffins recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Eggs – For egg-free, use 3 flax eggs (3 tbsp ground flax + 9 tbsp water, rest 10 minutes) or 3 chia eggs. Texture will be a bit more tender and bake time may increase a couple minutes.

Unsweetened almond milk –  You can substitute any type of milk here.

Unsweetened applesauce – Swap 1:1 with mashed ripe banana or pumpkin purée. You can also use ½ cup Greek yogurt and reduce the milk by 2–3 tbsp.

Avocado oil  – Use melted coconut oil, light olive oil, melted butter, or ghee in equal amounts.

Vanilla extract – Try ½ tsp almond extract or add 1–2 tsp lemon or orange zest for a bright, fruity flavor.

Oat flour – Make your own by blending rolled oats; use certified GF if needed. If you’re out, a 1:1 GF all-purpose blend can work, but the texture will be slightly different.

Almond flour – Cashew flour works 1:1. For nut-free, use sunflower seed flour 1:1 (note: it can turn a light green hue when baked—totally safe).

Coconut flour – Coconut flour is super absorbent and can’t be swapped 1:1. If you must omit it, use +½ cup almond flour and reduce milk by 2–3 tbsp, or use +⅓ cup oat flour plus 1 tbsp ground flax to help absorb moisture.

Natural cane sugar – Use coconut sugar or light brown sugar 1:1. Want less sweet? ½ cup works with a slightly tarter muffin. Liquid sweeteners aren’t ideal; if using maple syrup, reduce milk by ~3 tbsp and add 1 tbsp coconut or oat flour.

Fresh rhubarb – Frozen rhubarb (keep pieces small, don’t thaw; toss with 1 tsp oat flour). No rhubarb? Try strawberries or raspberries (keep pieces small and fold in gently).

Rolled oats – Quick oats create a finer crumb; for extra texture use ½ chopped nuts or seeds in place of some oats. Ensure certified GF if needed.

More muffin recipes you’ll love

• Flaxseed muffins
• Almond flour pumpkin muffins with streusel
• Easy oatmeal almond flour muffins

If you try this fluffy muffins recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather