The Best Lemon Cheesecake Muffins (with Streusel)

These incredibly moist Lemon Cream Cheese Muffins feature a bright, zesty lemon cake surrounding a rich, creamy cheesecake-like filling, all crowned with a buttery streusel. I’ve found that these are the perfect treat to brighten up any morning, and they disappear almost as soon as they cool. They bring together the best parts of a classic lemon muffin and a decadent cheesecake in one perfect handheld dessert.

Luscious lemon muffins topped with whipped cream and lemon zest, surrounded by fresh lemons on a white plate.

What Makes These Lemon Cream Cheese Muffins Truly Stand Out

These Lemon Cream Cheese Muffins are exceptional because they offer a perfect combination of bright, tangy lemon and a rich, creamy cheese filling. This creates a wonderful balance of flavors that unfolds with every single bite. The crunchy streusel on top adds a fantastic texture contrast to the soft muffin crumb.

A luscious lemon glaze provides the final touch with a sweet and tangy finish. With their moist, tender texture and vibrant citrus aroma, these muffins are not just beautiful to look at but also completely irresistible. They are an ideal choice for both a special breakfast and a satisfying dessert. Whether you are looking to impress your guests or just want to indulge in a special morning treat, these muffins are guaranteed to become a new favorite.

What You Need to Make This Lemon Cream Cheese Muffin Recipe

  • All-purpose flour This is the essential base for both our tender muffins and the crumbly streusel topping. To get the best texture, be sure to measure it correctly by spooning it into your measuring cup and leveling it off.
  • Light brown sugar and granulated sugar A mix of these sugars provides the perfect sweetness. They also contribute to a wonderfully tender crumb in the muffins and a classic crunch in the streusel.
  • Unsalted butter This ingredient adds rich flavor and essential moisture. You will need it melted for the streusel to form perfect crumbs and softened for the batter to create a light, airy texture.
  • Lemon zest and extract These are the sources of the muffin’s vibrant citrus flavor. Freshly grated lemon zest provides a bright, authentic taste that really makes these muffins shine.
  • Greek yogurt This is my secret for keeping the muffins incredibly moist. It also adds a subtle tang that beautifully complements the lemon.
  • Cream cheese This is the heart of our creamy filling. For the smoothest, most luxurious texture, make sure the cream cheese is full-fat and at room temperature before you start mixing.
  • Powdered sugar and lemon juice These simple ingredients come together to create the zesty glaze. It adds an extra pop of lemon flavor and a beautiful finish to the muffins.
Golden-brown lemon muffins with a crumbly streusel topping and a dollop of whipped cream, garnished with lemon zest

Steps to Make Lemon Cream Cheese Muffins

  1. Preheat & Prep First, preheat your oven to 425°F. This initial high heat gives the muffins a great initial rise. Line a standard 12-cup muffin pan with paper liners and set it aside for later. The amazing aroma that will soon fill your kitchen is something you can definitely look forward to.
  2. Streusel Topping In a medium bowl, mix together the flour, both granulated and brown sugars, and a pinch of salt. Pour the melted butter over the top. Use a fork to gently stir everything together until you see perfect, coarse crumbles form. Set the streusel aside while you prepare the other components.
  3. Muffin Batter In a separate bowl, whisk together the flour, baking powder, baking soda, and salt. Set this dry mixture aside. In a large bowl, use an electric mixer to beat the softened butter and sugar until the mixture becomes light and fluffy, which usually takes about 2 minutes. Add the eggs one at a time, then beat in the lemon zest, vanilla extract, and lemon extract. In a small bowl, stir the Greek yogurt and lemon juice together. Add this to the butter mixture and mix until just combined. Gently fold in the dry ingredients until a smooth batter forms, but be careful not to overmix.
  4. Cream Cheese Filling In another clean bowl, beat the softened cream cheese, sugar, and vanilla extract together. Continue mixing until the filling is completely smooth and creamy. This will be the delicious surprise center of your muffins.
  5. Assemble Muffins Now it is time to build your muffins. Spoon a layer of muffin batter into each liner, filling it about one-third of the way. Add a dollop of the cream cheese filling right into the center of each cup. Cover the filling with more muffin batter, so each cup is about two-thirds to three-quarters full. Finish by adding a generous sprinkle of the streusel crumbs over the top of each muffin.
  6. Bake Place the muffin pan into your hot oven and immediately turn the temperature down to 350°F. Bake for 22 to 25 minutes. You will know they are ready when the tops are a beautiful golden brown and a toothpick inserted into the cake part comes out clean.
  7. Cool & Glaze Let the muffins cool in the pan for 5 to 10 minutes before carefully transferring them to a wire rack to cool completely. While they are cooling, you can prepare the glaze. Whisk the powdered sugar and lemon juice together until smooth. Once the muffins are fully cool, drizzle the bright lemon glaze over the tops for the perfect finishing touch.

Tips for the Best Muffins

When you make these Lemon Cream Cheese Muffins, paying attention to the temperature of your ingredients is a key to success. For the streusel topping, you should use melted butter. This helps create the perfect crumbly texture that gives your muffins a delightful crunch. For the batter, however, using softened butter and room-temperature ingredients like eggs and cream cheese is very important. These ingredients mix together more smoothly and help create a lighter, fluffier muffin.

For the glaze, a good approach is to start with less lemon juice and add more a few drops at a time. Continue adding juice until you reach the consistency you like. This method gives you complete control over the thickness and tanginess of your glaze, making it a perfect final addition. Happy baking.

Close-up of a lemon muffin with a swirl of cream cheese frosting and sprinkled lemon zest, ready to be enjoyed.

Frequently Asked Questions

Can I use a different type of flour?

Yes, you can substitute whole wheat flour for a portion of the all-purpose flour for a heartier texture. Keep in mind that using all whole wheat flour will result in denser muffins. For a gluten-free version, use a quality 1-to-1 gluten-free baking blend.

How do I store these muffins?

Store the muffins in an airtight container. They will stay fresh at room temperature for up to 3 days. If you need to keep them longer, you can store them in the refrigerator for up to a week.

Can I freeze the muffins?

Absolutely. Let the muffins cool completely before placing them in a freezer-safe bag or container. They can be frozen for up to 3 months. When you are ready to enjoy one, just thaw it at room temperature.

Why did my cream cheese filling sink to the bottom?

If the cream cheese filling sinks, it could be that the muffin batter was too thin or the dollop of filling was too heavy. Make sure your batter is thick enough to support the filling, and try using a slightly smaller amount of filling in each muffin.

Can I make these into mini muffins?

Yes, this recipe works great for mini muffins. Simply use a mini muffin pan and reduce the baking time. Start checking for doneness around 12-15 minutes.

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Close-up of a lemon muffin with a swirl of cream cheese frosting and sprinkled lemon zest, ready to be enjoyed.

The Best Lemon Cheesecake Muffins (with Streusel)

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  • Author: Ryan Miller
  • Prep Time: 15 minutes
  • Cook Time: 25 minutes
  • Total Time: 40 minutes
  • Yield: 12 muffins
  • Category: Muffins
  • Method: Oven

Description

These Lemon Cream Cheese Muffins are a truly delightful treat, combining the bright, tangy freshness of lemon with a rich, creamy, cheesecake-like filling, finished with a sweet, buttery streusel topping and a zesty glaze they are utterly irresistible!


Ingredients

For the Streusel Crumb Topping

  • 1 cup (130 grams) all-purpose flour
  • ¼ cup (50 grams) light brown sugar, packed
  • ¼ cup (50 grams) granulated sugar
  • ¼ teaspoon (1 gram) fine sea salt
  • 6 tablespoons (90 grams) unsalted butter, melted

For the Lemon Muffins

  • 1 ½ cups (200 grams) all-purpose flour
  • ¼ teaspoon (1 gram) fine sea salt
  • ½ teaspoon (2 grams) baking powder
  • ¼ teaspoon (1 gram) baking soda
  • ⅓ cup (80 grams) unsalted butter, softened
  • ¾ cup (150 grams) granulated sugar
  • 2 large eggs, at room temperature
  • 2 tablespoons (10 grams) fresh lemon zest (from about 2 lemons)
  • 1 teaspoon (4 ml) pure vanilla extract
  • 1 teaspoon (4 ml) lemon extract
  • ⅔ cup (160 grams) plain Greek yogurt, full-fat recommended
  • 2 tablespoons (30 ml) fresh lemon juice

For the Cream Cheese Filling

  • 8 ounces (230 grams) full-fat cream cheese, at room temperature
  • ¼ cup (50 grams) granulated sugar
  • 1 teaspoon (4 ml) pure vanilla extract

For the Glaze

  • ¾ cup (100 grams) powdered sugar
  • 1 ½ to 2 ½ teaspoons (712 ml) fresh lemon juice

Instructions

Prepare for Baking

  1. Preheat your oven to 425°F (220°C).
  2. Line a standard 12-cup muffin pan with paper liners.

Make the Streusel Topping

  1. In a medium bowl, combine the flour, light brown sugar, granulated sugar, and salt, stirring to mix everything together.
  2. Pour the melted butter over the dry ingredients and stir gently with a fork until the mixture looks like coarse crumbs. Set this aside.

Prepare the Muffin Batter

  1. In a separate medium bowl, whisk together the flour, salt, baking powder, and baking soda. Set the dry ingredients aside.
  2. In a large bowl, using an electric mixer, beat the softened butter and granulated sugar together until the mixture is light and fluffy, about 2-3 minutes.
  3. Add the eggs one at a time, beating well after each addition until fully incorporated.
  4. Beat in the lemon zest, vanilla extract, and lemon extract until combined.
  5. In a small bowl, stir together the Greek yogurt and lemon juice.
  6. Add the yogurt mixture to the wet ingredients and mix until just combined.
  7. Gradually add the reserved dry ingredients to the wet ingredients. Mix on low speed until just combined. Be careful not to overmix the batter, a few small lumps are fine.

Prepare the Cream Cheese Filling

  1. In a clean medium bowl, beat the softened cream cheese with an electric mixer until smooth.
  2. Add the granulated sugar and vanilla extract and continue beating until the mixture is smooth and creamy.

Assemble the Muffins

  1. Spoon a layer of muffin batter into the bottom of each prepared muffin cup, filling it about one-third full.
  2. Place a dollop (about 1-2 tablespoons) of the cream cheese filling on top of the batter in each cup.
  3. Cover the cream cheese filling with more muffin batter, filling each cup about two-thirds full.
  4. Generously sprinkle the prepared streusel crumb topping over the batter in each cup.

Bake the Muffins

  1. Place the muffin pan in the preheated oven, then immediately reduce the oven temperature to 350°F (175°C).
  2. Bake for 22 to 25 minutes, or until the muffins are golden brown on top and a toothpick inserted into the cake part (avoiding the cream cheese filling) comes out clean.
  3. Let the muffins cool in the pan for a few minutes before transferring them to a wire rack to cool completely.

Make the Glaze

  1. While the muffins cool, prepare the glaze by whisking together the powdered sugar and 1 1/2 teaspoons of lemon juice in a small bowl until smooth.
  2. If the glaze is too thick, add more lemon juice a few drops at a time until it reaches a pourable consistency.
  3. Once the muffins are completely cool, drizzle the lemon glaze over the tops.

Notes

Gluten-Free Variation: To make these muffins gluten-free, substitute the all-purpose flour with a high-quality gluten-free flour blend that contains xanthan gum. Ensure all other ingredients, like baking powder, are certified gluten-free. The texture might differ slightly, but the wonderful lemon and cream cheese flavors will still shine through.


Nutrition

  • Serving Size: 1 muffin
  • Calories: 350
  • Sugar: 32g
  • Sodium: 120mg
  • Fat: 18g
  • Carbohydrates: 45g
  • Fiber: 1g
  • Protein: 5g
  • Cholesterol: 75mg

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