Gluten Free Rhubarb Muffins (Small Batch Recipe)

This small batch recipe for Gluten Free Rhubarb Muffins is perfect when you're craving something sweet but don’t want a dozen muffins hanging around. Each muffin is packed with tart rhubarb, bright lemon zest, and topped with a buttery oat streusel. They’re flavorful, easy to make, and come together with just a handful of pantry staples. Perfect for spring and summer baking

Recipe Ingredient Notes

Gluten Free Flour: I’ve tested these Gluten Free Rhubarb Muffins with a few different flour blends - my homemade mix, Bob’s Red Mill 1-to-1, and King Arthur Measure for Measure - and they all baked up with a lovely, light crumb. That’s not to say other gluten-free blends won’t work here; I just haven’t had a chance to try them yet.

Almond Flour: Almond flour adds a tender texture and helps keep these rhubarb muffins moist. It also pairs beautifully with the tartness of rhubarb, creating a subtle nutty backdrop. Need a nut-free option? You can swap the almond flour for more of the gluten-free flour blend used in the recipe.

Rhubarb: For the best results, choose stalks that are firm, crisp, and brightly colored with a slight gloss. Avoid any that look limp or have blemishes. You’ll usually find rhubarb in the produce section of your grocery store or at local farmers markets—and if you’re lucky, maybe even growing in your own backyard.

Sour Cream: Sour cream adds both richness and flavor to these muffins. I’ve tested the recipe with both sour cream and Greek yogurt, and they work equally well - so feel free to use whichever you have on hand. Dairy Free versions of those products can be used as well.

Milk: Just a splash helps loosen the thick batter, especially when using ingredients like sour cream or Greek yogurt. It ensures the muffins bake up with a soft, tender crumb and an even rise. I use 2% milk but whole milk or even a non dairy milk substitute will work.

What Is Rhubarb?

Rhubarb is technically a spring vegetable, though it's almost always used like fruit in baking. It grows in long, celery-like stalks that range in color from pale green to vibrant red. Only the stalks are edible - the leaves are toxic and should always be discarded.

What makes rhubarb stand out is its bold, tangy flavor. Raw, it’s intensely sour, but once cooked with sugar (or paired with naturally sweet fruits like strawberries), it mellows into something jammy, bright, and deeply flavorful. That sweet-tart contrast is exactly what makes rhubarb such a favorite in pies, crisps, cakes, and sauces.

Rhubarb is also a bit of a seasonal gem. It starts popping up in early spring and usually sticks around into early summer, making it feel like a short-lived treat worth savoring.

Gluten Free Oat Streusel

It's no secret that I love a good streusel topping. It adds the perfect bit of crunch and sweet, buttery flavor that pairs so well with a tender muffin. Plus, it makes them look extra inviting and adds something a little special to each bite.

1. Start by melting the butter - either in a small pot on the stove or in a microwave-safe bowl. Let it cool for a few minutes before using. (Dairy-free butter works just as well here.)
2. While the butter cools, whisk together the gluten-free flour, light brown sugar, rolled oats, cinnamon or some ground ginger, and kosher salt in a mixing bowl.
3. Once combined, drizzle in the melted butter and gently mix with a fork or small spatula until the mixture forms crumbles. Be careful not to overmix.
4. Pop the oatmeal streusel in the fridge while you make the gluten free rhubarb muffin batter. You can also freeze it for up to 3 months. It’s a handy topping that works beautifully on muffins, coffee cakes, or even cheesecakes.

Gluten Free Rhubarb Muffins

This recipe for Gluten Free Rhubarb Muffins comes together in no time. Plus, the muffin batter can be mixed by hand. No need to bring out the stand mixer or even an electric hand mixer.

1. For tall, bakery-style muffins, line every other cup in a 12-cup muffin pan - you’ll end up with 6 muffins total. Leaving space between each one gives them room to rise, helps them bake more evenly, and leads to those beautiful, high domed tops. It also keeps the pan from feeling crowded, so your muffins turn out fluffier and more like the ones you’d get at a bakery. (I use homemade muffin liners which are taller. IF you use regular muffin liners I would divide the muffin batter between 7-8 muffins cups)
2. Wash the rhubarb stalks under cold water and dry them with a paper towel. Remove both ends and any leaves as they are toxic.
3. Slice the Rhubarb stalks into rounds around ¼" wide round slices (kinda like cutting celery) and set them aside until needed. If the stalks are particularly thick, you might want to cut them lengthwise first and then into smaller pieces to ensure even cooking. Set it aside until needed.
4. In a small bowl, whisk or sift together the gluten free flour, almond flour, cornstarch, baking soda, baking powder, and kosher salt. Set aside.
5. In a large bowl, mix together the brown sugar (light or dark both work), granulated sugar, and lemon zest. Use your fingers or the back of a spoon to rub the zest into the sugar - this helps release the lemon’s natural oils and adds a little citrus flavor to the rhubarb muffins.

6. Add the room temperature egg and a generous teaspoon vanilla extract to the lemon sugar and whisk until smooth.
7. Once combined, add the sour cream and milk. Whisk everything together until well blended.
8. Add the oil to the mixture and whisk until fully combined.

9. Next add the dry ingredients to the wet ingredients and whisk to combine. You may need to switch to a flexible spatula if the batter becomes too thick to whisk.
10. Fold the sliced rhubarb into the muffin batter with a rubber spatula. Make sure they are evenly distributed.

11. Grab the prepared muffin pan and use a large cookie scoop to divide the rhubarb muffin batter between the liners. I like to fill them almost to the top - this helps create those beautiful, bakery-style domes.
12. Sprinkle each muffin with the gluten free oat streusel, then place the pan in the fridge while your oven preheats to 425°F. Letting the batter rest, even for just 15–30 minutes, gives the flour time to hydrate, which improves the texture. Bonus: cold batter rises higher in the oven!
13. Once the oven is fully preheated, bake the muffins at 425°F for 7 minutes. Then, without opening the oven door, lower the temperature to 350°F and continue baking for another 14–17 minutes, or until a toothpick inserted into the center comes out clean. The muffins are done when the tops spring back lightly to the touch. (Keep in mind, baking time may vary depending on your oven and how full you filled the liners - this timing is based on using homemade parchment liners.)
14. Let the muffins cool in the pan for 5–10 minutes, then transfer them to a wire rack to cool completely.

Storage & Freezing

Store the gluten free rhubarb muffins in an airtight container at room temperature for up to 3–4 days. Like most muffins, they’re best the day they’re baked - but these hold up surprisingly well and are just as tasty the next day.

To freeze, place the muffins on a baking sheet and freeze for 30 - 45 minutes until solid. Then transfer them to an airtight container or freezer bag and freeze for up to 3 months. When you're ready to enjoy one, let it thaw at room temperature. Or warm it up in the microwave for 15 - 30 seconds.

Variations of Gluten Free Rhubarb Muffins

• Rhubarb Sourdough Discard Muffins: Replace 30 grams of the gluten free flour along with the 30 grams of milk with a total of 60 grams of gluten free sourdough discard.
• Rhubarb Orange Muffins: Swap the lemon zest for orange zest. You could probably also replace the milk in the recipe with orange juice.
• Rhubarb Cream Cheese Swirl Muffins: Add a small dollop of sweetened cream cheese (mixed with a little vanilla and powdered sugar) to the center of each muffin before baking. You can use the cream cheese filling recipe from my Gluten Free Pumpkin Cream Cheese Muffins (you will only need HALF of that recipe!)
• Rhubarb Almond Muffins: Add about a ¼ teaspoon almond extract to the batter, and sprinkle sliced almonds over the muffin batter topping before baking. Almond and rhubarb are a beautiful match. (I would skip the streusel here)

Note about Salt in my Recipes

I use Diamond Kosher Crystal Salt in all of my recipes unless otherwise stated. If use use a different brand or kind of salt in your kitchen please adjust accordingly since some salts can be saltier. If you use Morton’s Kosher Salt please be aware that their salt granules are smaller in size, denser, and crunchier and twice as salty.

Baking in grams

I share my recipes in grams and by weight since baking by weight is the most accurate way to bake. Digital Scales are very affordable and easy to use. You can purchase them on Amazon for less than a set of measuring cups. For small amounts under 10 grams, I like to use this Precision Pocket Scale. Measuring cups are very inaccurate which can cause significant errors when it comes to gluten-free baking or baking in general. Especially since I bake with gluten-free flours which weigh differently than “regular” flours. I do provide some ingredients like spices and leavening agents in measuring spoons. To learn more about Baking with a digital scale, make sure to check out my post about Baking by weight.

Note about Ovens and Oven Temperatures

All my recipes are tested and developed with a conventional oven. I always bake my baked goods on the rack placed in the MIDDLE of my oven. This way the heat coming from the bottom will not burn my baked goods.

If you are baking with convection (fan-forced), please adjust the recipes accordingly. Convection oven can cause baked goods to dry out quickly and still be raw inside. Since takes at least 15-20 minutes for a standard American Oven to be fully preheated. I highly recommend investing in an Oven Thermometer.

Substitutions and Modifications

Any dietary or ingredient modifications/substitutions to this recipe may alter the end result in appearance and taste. I test my recipes several times as published in this post and The Gluten Free Austrian Blog is not responsible for the outcome of any recipe you find on our website.