Homemade Paleo Strawberry Rhubarb Muffins

If you ask me, strawberry rhubarb is one of the best flavor combinations out there.

These paleo muffins bring together tart rhubarb and sweet strawberries in a tender almond flour base that’s naturally gluten-free. A touch of honey and warm cinnamon balance out the fruit, while chopped almonds on top add a nice crunch.

They’re made without any refined sugar or grains, just simple ingredients that work together. A splash of lemon juice brightens everything up, and the result is a breakfast treat that tastes like spring.

It’s an easy recipe that’s perfect for weekend mornings or meal prep for the week ahead.

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What Kind of Rhubarb Should I Use?

Fresh rhubarb is your best bet for these muffins, and you’ll find it in season during spring and early summer at most grocery stores and farmers markets. Look for stalks that are firm and crisp, avoiding any that feel soft or look dried out at the ends. The color can range from light pink to deep red, and while the redder stalks might look prettier, the color doesn’t actually affect the flavor much. Make sure to trim off and discard the leaves if they’re still attached, as they’re toxic – you only want to use the stalks for baking. If fresh rhubarb isn’t available, frozen rhubarb works just fine, though you should thaw it first and pat it dry with paper towels to remove excess moisture.

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Options for Substitutions

These paleo muffins are pretty forgiving when it comes to swaps, though a few ingredients really need to stay put:

• Almond flour: This is the base of the recipe, so don’t substitute it. Almond flour is what keeps these muffins paleo-friendly and gives them the right texture. Other nut flours or regular flour won’t work the same way.
• Rhubarb: If rhubarb isn’t in season or you can’t find it, you can use all strawberries instead (so 1 1/2 cups total). You could also try diced apples or blueberries, though the tartness will be different.
• Arrowroot: Tapioca starch works as a direct 1:1 swap for arrowroot. In a pinch, you could use cornstarch, but that’s not paleo-compliant if you’re strictly following the diet.
• Honey: Maple syrup works great as a substitute using the same amount. If you’re not strictly paleo, coconut sugar would also work, though you might need to add a tablespoon or two of milk to maintain moisture.
• Coconut sugar: For the topping, you can use regular sugar or skip it entirely. The muffins will still taste great without that little sprinkle on top.

Watch Out for These Mistakes While Baking

The biggest mistake with paleo muffins is overmixing the batter once you add the wet and dry ingredients together, which can make your muffins dense and gummy – just stir until everything is combined and you still see a few streaks of flour.

Since almond flour behaves differently than regular flour, these muffins can easily overbake and dry out, so start checking them at 22 minutes and remove them as soon as a toothpick comes out with just a few moist crumbs.

Another common issue is that rhubarb releases a lot of moisture during baking, so make sure to cut it into small, uniform pieces (about 1/4 inch) and pat both the strawberries and rhubarb dry with a paper towel before folding them into the batter.

Finally, let the muffins cool in the pan for at least 10 minutes before removing them, as paleo muffins are more delicate when hot and can fall apart if you try to take them out too soon.

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What to Serve With Strawberry Rhubarb Muffins?

These muffins are perfect for breakfast or brunch alongside a hot cup of coffee or tea. I love serving them with a simple fruit salad made with fresh berries and melon, or even just sliced bananas with a drizzle of almond butter. They also pair nicely with scrambled eggs and bacon if you’re looking for a more filling breakfast spread. For an afternoon snack, try them with a glass of cold almond milk or your favorite dairy-free milk alternative.

Storage Instructions

Store: Keep these muffins in an airtight container at room temperature for up to 3 days, or in the fridge for about a week. Since they’re made with almond flour, they tend to stay moist longer than regular muffins, which is a nice bonus!

Freeze: These muffins are perfect for freezing. Just let them cool completely, then wrap each one individually in plastic wrap or parchment paper before placing them in a freezer bag. They’ll keep for up to 3 months, and you can grab one whenever you need a quick breakfast or snack.

Thaw: To enjoy a frozen muffin, simply leave it on the counter for about 30 minutes to thaw at room temperature. If you’re in a hurry, you can microwave it for 20-30 seconds on medium power. They taste great at room temp or slightly warmed!

Estimated Nutrition

Estimated nutrition for the whole recipe (without optional ingredients):

• Calories: 1950-2100
• Protein: 48-54 g
• Fat: 120-135 g
• Carbohydrates: 180-200 g

Ingredients

For the muffin batter:

• 1 cup strawberries (finely chopped, about 1/4-inch pieces)
• 1 cup rhubarb (sliced into thin 1/4-inch half-moons)
• 3 1/4 cups almond flour (I always use Blue Diamond for the finest texture)
• 7 tbsp arrowroot
• 3/4 tsp baking soda
• 1/2 tsp salt
• 3 eggs (room temperature, about 70°F)
• 1/2 cup + 2 tbsp honey (I recommend Nature Nate’s raw honey)
• 1 1/2 tsp vanilla
• 1 1/2 tsp lemon juice
• 1/4 tsp ground cinnamon

For the topping:

• 3 tbsp almonds (roughly chopped for a better crunch)
• 1 tsp coconut sugar

Step 1: Prepare Mise en Place and Preheat

• 1 cup strawberries, finely chopped
• 1 cup rhubarb, sliced thin
• 3 tbsp almonds, roughly chopped

Position your oven rack in the middle and preheat to 350°F.

While the oven heats, finely chop the strawberries into roughly 1/4-inch pieces and slice the rhubarb into thin 1/4-inch half-moons—keeping them uniform in size ensures even cooking throughout the muffins.

Line your muffin pan with paper liners.

Chop the almonds roughly for the topping and have all ingredients measured and ready before you begin mixing.

Step 2: Mix Dry Ingredients

• 3 1/4 cups almond flour
• 7 tbsp arrowroot
• 3/4 tsp baking soda
• 1/2 tsp salt
• 1/4 tsp ground cinnamon

In a medium bowl, whisk together the almond flour, arrowroot, baking soda, salt, and ground cinnamon.

This ensures the leavening agent and salt are evenly distributed throughout the flour base, preventing any pockets of baking soda that could create unpleasant metallic flavors.

Set the dry mixture aside.

Step 3: Combine Wet Ingredients

• 3 eggs, room temperature
• 1/2 cup + 2 tbsp honey
• 1 1/2 tsp vanilla
• 1 1/2 tsp lemon juice

In a separate bowl, whisk together the room-temperature eggs, honey, vanilla, and lemon juice until well combined and slightly frothy—this incorporates air into the batter, which helps the muffins rise and achieve a tender crumb.

The room-temperature eggs mix more easily and create a smoother batter.

Step 4: Combine Wet and Dry Mixtures

• wet ingredient mixture from Step 3
• dry ingredient mixture from Step 2

Pour the wet ingredient mixture from Step 3 into the bowl with the dry ingredient mixture from Step 2, then gently stir until just combined.

I like to fold rather than vigorously mix at this stage—overmixing develops gluten in almond flour, which can make the muffins dense and tough.

Stop as soon as you don’t see streaks of dry flour.

Step 5: Fold in Fruit and Fill Muffin Cups

• prepared strawberries and rhubarb from Step 1
• combined batter from Step 4

Gently fold the chopped strawberries and sliced rhubarb from Step 1 into the batter using a spatula, being careful not to overwork the batter.

Divide the batter evenly among the lined muffin cups, filling each about three-quarters full.

The batter will rise slightly as it bakes, so don’t overfill.

Step 6: Top and Bake

• 3 tbsp almonds from Step 1
• 1 tsp coconut sugar

Sprinkle the roughly chopped almonds evenly over the top of each muffin, then sprinkle the coconut sugar over the almonds.

This creates a pleasant textured topping that won’t burn in the oven.

Bake for 22–26 minutes, until a toothpick inserted into the center of a muffin comes out with just a few moist crumbs (not wet batter).

The muffins should be golden-brown and spring back when lightly touched.

Step 7: Cool and Serve

Remove the muffin pan from the oven and let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely.

This prevents the bottoms from becoming soggy from condensation while still allowing air circulation.

Homemade Paleo Strawberry Rhubarb Muffins

Delicious Homemade Paleo Strawberry Rhubarb Muffins recipe with step-by-step instructions.

Print Recipe Pin Recipe

Prep Time 15 minutes mins

Cook Time 25 minutes mins

Total Time 42 minutes mins

Servings 12 muffins

Calories 2025 kcal

Ingredients

  

For the muffin batter::

• 1 cup strawberries (finely chopped, about 1/4-inch pieces)
• 1 cup rhubarb (sliced into thin 1/4-inch half-moons)
• 3 1/4 cups almond flour (I always use Blue Diamond for the finest texture)
• 7 tbsp arrowroot
• 3/4 tsp baking soda
• 1/2 tsp salt
• 3 eggs (room temperature, about 70°F)
• 1/2 cup + 2 tbsp honey (I recommend Nature Nate's raw honey)
• 1 1/2 tsp vanilla
• 1 1/2 tsp lemon juice
• 1/4 tsp ground cinnamon

For the topping::

• 3 tbsp almonds (roughly chopped for a better crunch)
• 1 tsp coconut sugar

Instructions

 

• Position your oven rack in the middle and preheat to 350°F. While the oven heats, finely chop the strawberries into roughly 1/4-inch pieces and slice the rhubarb into thin 1/4-inch half-moons—keeping them uniform in size ensures even cooking throughout the muffins. Line your muffin pan with paper liners. Chop the almonds roughly for the topping and have all ingredients measured and ready before you begin mixing.
• In a medium bowl, whisk together the almond flour, arrowroot, baking soda, salt, and ground cinnamon. This ensures the leavening agent and salt are evenly distributed throughout the flour base, preventing any pockets of baking soda that could create unpleasant metallic flavors. Set the dry mixture aside.
• In a separate bowl, whisk together the room-temperature eggs, honey, vanilla, and lemon juice until well combined and slightly frothy—this incorporates air into the batter, which helps the muffins rise and achieve a tender crumb. The room-temperature eggs mix more easily and create a smoother batter.
• Pour the wet ingredient mixture from Step 3 into the bowl with the dry ingredient mixture from Step 2, then gently stir until just combined. I like to fold rather than vigorously mix at this stage—overmixing develops gluten in almond flour, which can make the muffins dense and tough. Stop as soon as you don't see streaks of dry flour.
• Gently fold the chopped strawberries and sliced rhubarb from Step 1 into the batter using a spatula, being careful not to overwork the batter. Divide the batter evenly among the lined muffin cups, filling each about three-quarters full. The batter will rise slightly as it bakes, so don't overfill.
• Sprinkle the roughly chopped almonds evenly over the top of each muffin, then sprinkle the coconut sugar over the almonds. This creates a pleasant textured topping that won't burn in the oven. Bake for 22–26 minutes, until a toothpick inserted into the center of a muffin comes out with just a few moist crumbs (not wet batter). The muffins should be golden-brown and spring back when lightly touched.
• Remove the muffin pan from the oven and let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to cool completely. This prevents the bottoms from becoming soggy from condensation while still allowing air circulation.