Meyer Lemon Muffins
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This recipe for Meyer Lemon Muffins makes moist and fluffy lemon muffins. I fill them with mini chocolate chips and top these with a traditional crumb topping and a sweet and zesty lemon glaze!
If you love organic muffins, be sure to check out some of my other favorites like my Eggless Banana Raspberry Muffins, Coffee Cake Muffins, or my make some muffins for your pup with my Healthy Dog Muffins Recipe.

Table of Contents
If you love lemon and chocolate together, you will love these homemade muffins! While most people combine chocolate and orange, I think chocolate and lemon is an insanely better pairing. These lemon muffins use Meyer lemons for a sweet lemon flavor combined with mini chocolate chips in a moist and fluffy mufifn.
I top these lemon muffins with a traditional streusel topping for that perfect crumble top. And, they are finished off with a sweet and slightly tart lemon glaze. These organic muffins are a quick and easy recipe that I love making on a weekend morning.

Why You'll Love This Recipe
Seasonal Treat: This is a special recipe because it uses Meyer lemons, which are only in season for part of the year! I love seasonal recipes as it makes them special and nostalgic! This recipe for Meyer Lemon Muffins uses the sweetness of Meyer lemons combined with mini chocolate chips, a crumb topping, and a sweet glaze.
Crumb Topping: You will love this recipe for Meyer Lemon Muffins because it has a crumb topping! I absolutely love crumb toppings on homemade muffins, the extra sweetness and texture combined with a soft and fluffy muffin is just so good!
Chocolate + Lemon: I love chocolate and lemon together. The light and sweetness of the lemons combined with rich and decadent chocolate is a home run. I use mini chocolate chips in these Meyer Lemon Muffins so you get a small bit of chocolate in each bite, making it just enough!
Organic Muffins: While you can go out to the cafe or grocery store and pick up lemon muffins, they most likely will not have high quality organic ingredients. When you make organic muffins at home you're not only prioritizing your health and wellness, but also getting a superior tasting muffin!

Ingredients
- Butter: I use Organic Valley Salted Butter, you can use your favorite.
- Cane Sugar: I use organic cane sugar as it's less processed than granulated white sugar.
- Eggs: Use large eggs.
- Lemon Flavor: I add in organic lemon flavor to ensure these lemon muffins are bursting with lemon in every bite!
- Milk: Use whole milk for the best flavor. I also prefer organic and grassfed for the most nutrients.
- Cream Cheese: I use Organic Valley Cream Cheese, which provides a slight tang that pairs perfectly with the zesty lemon and rich chocolate. You can use block or tub cream cheese, either works.
- All Purpose Flour: I use Cairnspring Mills.
- Baking Powder: Be sure to use baking powder, not soda. This will create tall and fluffy homemade muffins. Be sure to check out my post the Difference Between Baking Soda and Baking Powder for more info on leavening agents.
- Salt: Use fine sea salt.
- Chocolate Chips: I use organic mini dark chocolate chips, which are perfect for homemade muffins. The mini chocolate chips are so much lighter than traditional size, and this helps them not sink the muffin batter! You also are guaranteed to get chocolate chips in every single bite.
- Light Brown Sugar: I use my homemade organic light brown sugar for the topping, but store bought also works.
- Walnuts: I use organic raw walnuts in the streusel topping.
- Powdered Sugar: Be sure you are using sifted powdered sugar to get a perfectly smooth glaze without clumps.
- Meyer Lemons: I use Meyer lemons, but if you can only get regular lemons those are okay too.

Tools Needed
- Scale: Always use a digital food scale for the best results.
- Stand Mixer: I use my stand mixer for ease, but if you prefer to use a hand mixer, you can do that too.
- Muffin Pan: You'll need a muffin (or cupcake) pan to bake these organic muffins.
- Mixing Bowl: You'll need a large mixing bowl to mix up the topping.
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Step by Step Instructions
Step 1
Preheat the oven to 350°F. Line two muffin tins with liners.
Step 2
To make the batter: In the bowl of a stand mixer fitted with the paddle attachment, add the butter, cane sugar, and lemon flavor and mix on low until combined and there are no chunks. Add the eggs, milk, and cream cheese and mix until combined.
In a separate bowl, add the flour, baking powder, and sea salt and whisk together. With the mixer on low, slowly add in the flour mixture and mix until a smooth batter forms, scraping down the sides of the bowl as needed. Add the mini chocolate chips and mix to combine completely. Fill the muffin tins full.
Step 3
To make the topping: In large bowl, add the melted butter, flour, light brown sugar, cane sugar, and chopped walnuts and mix together until a paste forms.
Using your hands, crumble the topping onto the tops of the muffins.
Step 4
Bake for 20 to 25 minutes or until a wooden pick inserted in center comes out clean. Allow to cool completely in the tins. (If you're baking at high altitude make sure to check the recipe Notes for high altitude baking instructions).
Step 5
To make the glaze: In a small bowl, add the powdered sugar, lemon juice, and lemon zest and whisk together until you have a smooth glaze. Drizzle over the tops of the muffins.

FAQ's
Meyer lemons are a type of lemon. They are actually native to China and are a hybrid fruit, a cross between a citron and mandarin/pomelo.
Meyer lemons differ in flavor, taste, and looks from traditional lemons. The flavor or Meyer lemons is much more sweet than traditional lemons, while your standard lemon is pretty tart. This is part of the reason I love Meyer lemons so much, as they provide a sweet lemon flavor.
They are smaller and more round than traditional lemons. They also differ in color, Meyer lemons tend to be darker yellow and even have a little orange tint to them, while traditional lemons are bright yellow. Their skin is also softer and smoother than traditional lemon skin that has that texture. For more info, read my article Difference Between Lemons and Meyer Lemons.
Yes, you can always substitute one for the other – it's still a lemon so it will work the same in any recipe. But, depending on which type you use, you will have different results with the recipe as far as the flavor profile goes. Meyer lemons will be sweeter and regular lemons will have a more tart and zesty lemon flavor.

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Meyer Lemon Muffins
Ingredients
Batter
- 113 grams salted butter (softened)
- 113 grams cane sugar
- 1 teaspoon lemon flavor
- 2 large eggs (room temperature)
- ½ cup milk (room temperature)
- 57 grams cream cheese (room temperature)
- 212 grams all purpose flour
- ¾ teaspoon baking powder
- ½ teaspoon fine sea salt
- 170 grams mini dark chocolate chips
Topping
- 57 grams salted butter (melted)
- 64 grams all purpose flour
- 28 grams light brown sugar (packed)
- 28 grams cane sugar
- 64 grams walnuts (chopped)
Glaze
- 142 grams powdered sugar (sifted)
- 2 tablespoons Meyer lemon juice
- zest of 1 Meyer lemon
Instructions
- Preheat the oven to 350°F. Line two muffin tins with liners.
- To make the batter: In the bowl of a stand mixer fitted with the paddle attachment, add the butter, cane sugar, and lemon flavor and mix on low until combined and there are no chunks. Add the eggs, milk, and cream cheese and mix until combined.
- In a separate bowl, add the flour, baking powder, and sea salt and whisk together. With the mixer on low, slowly add in the flour mixture and mix until a smooth batter forms, scraping down the sides of the bowl as needed. Add the mini chocolate chips and mix to combine completely. Fill the muffin tins full.
- To make the topping: In large bowl, add the melted butter, flour, light brown sugar, cane sugar, and chopped walnuts and mix together until a paste forms.
- Using your hands, crumble the topping onto the tops of the muffins.
- Bake for 20 to 25 minutes or until a wooden pick inserted in center comes out clean. Allow to cool completely in the tins.
- To make the glaze: In a small bowl, add the powdered sugar, lemon juice, and lemon zest and whisk together until you have a smooth glaze. Drizzle over the tops of the muffins.
- Store in an airtight container for up to 3 days.
Notes
Nutrition
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