Lemon Muffins

Lemon Muffins with Lemon Cream Cheese Filling are made from scratch, are refreshing, zesty, sweet, and tart, with a moist cake layer, a sweet lemon cream cheese layer, and topped with a crumb topping. An absolutely delicious breakfast, brunch, or afternoon snack recipe.

A lemon muffin on a round white plate with more muffins in the background.

Lemon muffins are always a great treat for any occasion. They’re sweet, moist, and loaded with that zesty lemon flavor. I’ve been making muffins like these for years, and although everyone loves them, even great recipes can get boring. So I thought I’d add even more lemon goodness to these muffins by stuffing them full of lemon cream cheese! It was the best decision I’ve made. I whipped up a batch of these the last time my daughter’s family came to visit, and it was extremely well received. In fact, this is going to be a part of my regular muffin rotation from now on. With all its delicious flavor and textures, I think it’ll have pride of place in your recipe collection, as well. They might not look the best but they are absolutely delicious!

Lemon Muffins

This recipe is a new twist on an old favorite, so you’ll find everything you love about lemon muffins and then some. It starts with a delicious lemon batter for the muffins made with lemon Greek yogurt for extra moistness. Then, I add a lemon cream cheese topping that’s tangy, sweet, and zesty. Finally, I top it with an easy and sweet crumb topping and bake the muffins up to golden perfection. When it’s all said and done, I have a batch of muffins with a classic, tender muffin base, a deliciously tangy lemon layer, and the extra sweetness of the crumb topping. It all comes together to create muffins that are loaded with both flavor and textures – the full snacking experience! Whip up a batch and serve them for a sweet breakfast, brunch, or addition to any potluck.

Why You’ll Love This Lemon Muffin Recipe

  • They’re absolutely delicious, and they’re sweet, tart, and so moist.
  • They have a lemon cream cheese layer and a crumb topping that you can’t beat.
  • They’re the perfect sweet breakfast, brunch, or dessert treat.

Why are These the Best Lemon Muffins?

Even without the lemon cream cheese mixture, these muffins are moist and tender. However, when you add that cream cheese layer and top it with the crumble, you get a muffin like you’ve never had before. The extra richness of the lemon layer adds both moisture and luscious, lemony flavor to the muffins that really skyrockets them to another level. They’re also easy to make, and as we all know, an easy recipe (that’s also delicious) is a great recipe!


  • Don’t overmix your muffin batter. As soon as the ingredients are combined, stop mixing. Lumps are fine. Overmixing leads to tough muffins.
  • Don’t overfill your muffin cups. You need space for that delicious lemon layer.
  • Use cold butter for the crumble topping. You want a crumbly texture, not a smooth one.


  • Try using your favorite fruit flavors for the muffin batter by replacing the lemon Greek yogurt with other fruity variations.
  • You can change the lemon filling to other flavors by using different extracts like blueberry extract.
A close up of a lemon muffin with a bite taken out of it.

What to Serve with Lemon Muffins

The great thing about muffins is that they make a deliciously sweet breakfast on their own or as a sweet addition to your savory favorites. Try serving up your muffins with:

  • Milk
  • Coffee
  • Orange juice
  • Eggs
  • Bacon
  • Sausage
  • Omelets
  • Breakfast skillets


Are muffins better with oil or butter?

Neither one is better. They’re just different. Butter gives muffins more of a crumb to the texture. However, oil makes a muffin that’s moister. Either works well. You can also split the difference and use a half-and-half mixture of butter and oil.

What does oil do in a muffin recipe?

Oil adds extra moisture to the muffins. While both oil and butter are fats, the natural liquidity of the oil makes for moister muffins.

What is the role of yogurt in baking?

Yogurt does several things in baking. First, it makes for very moist baked goods. In addition, its tang gives baked goods a classic, old-fashioned flavor. Finally, its acidity helps activate baking soda, which helps baked goods be as light and fluffy as possible.

How long will homemade muffins with cream cheese last?

Muffins like these will last for about 3 days in the refrigerator. Yes, they must be refrigerated.

Can you freeze lemon muffins?

Yes, you can. Store them in an airtight, freezer-safe container and freeze for up to a month.

Two muffins stacked on top of each other with a bite out of the top muffin.

Storing Instructions

Store these muffins in an air-tight container in the refrigerator for up to 3 days. For longer storage, freeze them for up to a month. Chill the muffins completely and wrap them in a double layer of cling wrap. Then, place them in an airtight, freezer-safe container and freeze.

Lemon Muffins Ingredients

This recipe uses basic ingredients that you’ll find in your pantry and at your local grocery store.

  • All-purpose flour
  • Baking powder
  • Baking soda
  • Salt
  • Vegetable oil
  • Sugar
  • Large egg + egg yolk
  • Lemon Greek yogurt
  • Fresh lemon juice
  • Lemon zest
  • Cream cheese
  • Vanilla extract
  • Butter

For the actual measurements and ingredients, scroll to the recipe card at the bottom of this post.

How to Make Lemon Muffins

Making these muffins is incredibly simple. You’ll only need a few minutes to make them!

Step 1: Prep

Preheat the oven to 350 degrees. Add paper muffin liners to a muffin pan or lightly spray the tin with nonstick cooking spray. Set aside.

Step 2: Combine the Dry Muffin Ingredients

Whisk the flour, baking powder, baking soda, and salt together in a medium bowl.

Step 3: Combine the Wet Muffin Ingredients

In large mixing bowl, beat the oil and sugar for 2 minutes. Then, beat in the egg. Finally, add the lemon yogurt, lemon juice, and lemon zest and mix until combined.

Step 4: Complete the Batter

Add the dry ingredients to the large bowl with the wet ingredients and mix until just combined. Then, fill each muffin tin 2/3 full.

Step 5: Make the Cream Cheese Filling

Beat the cream cheese, sugar, egg yolk, lemon juice, lemon zest, and vanilla together in a small mixing bowl. Add the mixture to each muffin tin.

Step 6: Make the Crumb Topping

Mix the butter, flour, and sugar together in a small bowl until crumbly. Then, add the topping to each muffin.

Step 7: Bake

Bake the muffins for 30 – 35 minutes or until toothpick inserted comes out clean. Remove and let cool on a wire rack for 10 minutes before serving. Enjoy!

A double collage photo of lemon muffins.

Try This Delicious Lemon Muffin Recipe Today

These lemon muffins are super moist, loaded with rich lemon flavor, a cream cheese layer, and topped with a sweet crumble, making a muffin recipe that’s as full of texture as it is deliciousness. Give these a try, and I guarantee you’ll find yourself making them again and again. They’re great for parties, breakfast, or just because.

A three photo collage of lemon muffins.

More Delicious Lemon Dessert Recipes You’ll Enjoy

Cream Cheese Lemonade Pie – This delicious zesty, tart, lemony pie is creamy, super easy to make and is one of the most popular desserts on the blog. 

Luscious Lemon Cheesecake – This lip smacking, mouthwatering, luscious cheesecake is full of lemony flavor and is an absolutely incredible lemon cheesecake recipe.

Lemon Pastries – These lemon pastries are easy to make and uses simple ingredients, baked to golden perfection with a lemon glaze drizzle.

And, here is a delicious Lemon Pretzel Dessert from Deliciously Seasoned that tastes amazing!

Lemon Muffins

Great Grub, Delicious Treats

These delicious lemon muffins are super moist, topped with a layer of lemon cream cheese filling and then a crumb topping, and baked to perfection. So lemony, so flavorful and so delicious!

Prep Time 25 mins

Cook Time 30 mins

Total Time 55 mins

Course Dessert

Cuisine American

Servings 12 Muffins

Calories 371 kcal


Lemon Muffins

  • 1 ½ cup all purpose flour
  • ½ teaspoon baking powder
  • ¼ teaspoon baking soda
  • ¼ teaspoon salt
  • ½ cup vegetable oil
  • ¾ cup sugar
  • 1 large egg
  • ½ cup lemon Greek yogurt
  • 2 tablespoons lemon juice
  • 1 tablespoon lemon zest

Lemon Cream Cheese Filling

  • 8 ounces cream cheese
  • cup sugar
  • 1 egg yolk
  • 2 teaspoon fresh lemon juice
  • 1 tablespoon lemon zest
  • 1 tsp vanilla extract

Crumb Topping

  • cup all purpose flour
  • cup sugar
  • ¼ cup butter


Lemon Muffins

  • In a medium bowl, whisk flour, baking powder, baking soda, and salt together until combined.

  • In another bowl, beat oil and sugar together for 2 minutes then beat in egg.

  • Next, add lemon yogurt, lemon juice and lemon zest, and mix until combined.

  • Add dry ingredients into the wet ingredients and mix until just combined.

  • Spoon batter into paper liners 2/3rds full.

Lemon Cream Cheese Filling

  • In a small mixing bowl, beat cream cheese, sugar, egg yolk, lemon juice, lemon zest and vanilla together until combined.

  • Add a layer of cream cheese mixture on top of each muffin.

Crumb Topping

  • In a small bowl, add flour, sugar, and butter together until crumbly.

  • Add crumb topping and bake in preheated oven for 30-35 minutes.

  • Remove from oven. Let cool for 10 minutes before serving. Can serve warm or cold.


Nutritional values are approximate.


Please note that these values can change with different brands and any modifications made to the recipe. For the most accurate information, use a nutritional calculator with the exact brands and measurements.

Recipe inspired from Lord Byron’s Kitchen


Calories: 371kcalCarbohydrates: 43gProtein: 5gFat: 21gSaturated Fat: 8gCholesterol: 60mgSodium: 171mgFiber: 1gSugar: 25gVitamin C: 3mgCalcium: 45mgIron: 1mg

Keyword Lemon Cream Cheese Muffins, Lemon Cupcakes, Lemon Muffins

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A muffin on a white plate with more muffins in the background.
Two muffins stacked on top of each other with the top muffin with a bite taken out of it.

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