Super Moist Berry Cheesecake Muffins

Featured in Sweet Moments of Joy.

These berry cream cheese muffins are the perfect balance of sweetness and texture. Bursting with fresh blueberries and raspberries, each muffin has a creamy cheesecake filling and a crunchy streusel topping. The Greek yogurt in the batter ensures a moist crumb, while the glaze adds a decorative touch of sweetness. Whether for breakfast, dessert, or a snack, these easy-to-make muffins deliver flavor and indulgence in every bite. Great for summer berry season or anytime you crave something fruity and creamy.

Barbara Chef
Updated on Sat, 03 May 2025 13:46:24 GMT
A cupcake with berries and cream. Pin it
A cupcake with berries and cream. | gracefulflavors.com

This berry cream cheese muffin recipe has become my weekend breakfast tradition, bringing together the perfect balance of juicy summer berries, creamy cheesecake filling, and buttery streusel topping all in one irresistible treat.

I originally created these when my sister visited last summer and had an abundance of farmers market berries about to spoil. Now they're requested at every family gathering and holiday brunch.

Ingredients

  • All purpose flour: Forms the backbone of both the muffin batter and streusel topping creating perfect texture
  • Greek yogurt: Adds incredible moisture and slight tanginess that balances the sweetness
  • Fresh berries: Provide bursts of juicy flavor and natural sweetness. Use a mix of blueberries and raspberries for color contrast
  • Cream cheese: Creates the luxurious cheesecake filling that makes these muffins special. Look for full fat for best results
  • Light brown sugar: In the streusel adds a subtle caramel note that plain sugar cannot match
  • Vanilla extract: Enhances all the flavors without overpowering. Use pure, not imitation, for best results

Step-by-Step Instructions

Prepare the Streusel:
Combine flour, brown sugar, and salt in a bowl until evenly distributed. Pour in the melted butter and work it with a fork until you have a crumbly mixture with pieces ranging from pea-sized to slightly larger. The streusel should hold together when squeezed but still break apart easily.
Mix the Cream Cheese Filling:
Beat room temperature cream cheese until smooth and free of lumps—this is crucial for a silky filling. Add sugar, vanilla, and cornstarch, mixing just until combined. The cornstarch stabilizes the filling so it doesn’t become runny during baking.
Create the Muffin Batter:
Whisk the dry ingredients (flour, baking powder, and salt) thoroughly to ensure even distribution. In a separate bowl whisk the egg and sugar until pale and slightly thickened, about 1 minute. Incorporate the yogurt, oil, and vanilla until the mixture looks smooth and consistent. The yogurt is key here, creating an incredibly moist crumb.
Combine and Add Berries:
Fold the wet ingredients into the dry ingredients using gentle strokes to avoid overmixing, which leads to tough muffins. When just combined, carefully fold in about half the berries, allowing some to break slightly to flavor the batter while keeping others whole for bursts of fruit.
Assemble the Layers:
Add a small amount of batter to each muffin cup, spreading it slightly up the sides to create a nest. Spoon the cream cheese filling into the center, being careful not to let it touch the sides of the liner. This creates that perfect surprise center when bitten into.
Finish and Bake:
Top with remaining batter, additional berries, and generous streusel, pressing gently to adhere. The temperature shift from 425°F to 350°F creates an initial rise followed by even baking for perfectly domed tops.
A cupcake with berries on top. Pin it
A cupcake with berries on top. | gracefulflavors.com

The cream cheese filling was inspired by my grandmother’s cheese danish recipe she used to make every Christmas morning. I can still picture her gently folding berries into the batter, warning us kids not to overmix or we’d lose those beautiful pockets of fruit.

Perfect Berry Selection

The type of berries you choose dramatically impacts these muffins. While the recipe calls for blueberries and raspberries, try blackberries, strawberries, or even cranberries in fall. Fresh berries will always provide the best texture and flavor, but in winter frozen berries work well too. Just fold them in while still frozen to prevent bleeding into the batter. The juiciest berries are those that are fragrant, in season, and deeply colored through to their center.

Make Ahead Options

These muffins are perfect for batch preparation. Prepare the streusel up to 3 days ahead, storing it in an airtight container in the refrigerator. The muffin batter can be mixed the night before without berries—just cover tightly and refrigerate. In the morning, fold in the berries and proceed with assembly. Baked muffins stay fresh at room temperature for 2 days in an airtight container or refrigerated for up to 5 days. Simply warm them for 15 seconds in the microwave before serving to revive that freshly baked taste.

A cupcake with berries on top. Pin it
A cupcake with berries on top. | gracefulflavors.com

Serving Suggestions

While these muffins are delicious on their own, create a stunning brunch spread by serving them slightly warm alongside a fruit platter, fresh whipped cream, and hot coffee. For dessert, warm a muffin and top with a small scoop of vanilla ice cream, letting it melt slightly into the berries and streusel. These also make thoughtful gifts packaged in kraft paper boxes tied with twine, especially during berry season when their flavor is at its peak.

Frequently Asked Questions

→ Can I use frozen berries instead of fresh?

Yes, you can use frozen berries. Make sure to toss them in a bit of flour to prevent them from sinking and to minimize excess moisture in the batter.

→ What substitutes can I use for Greek yogurt?

You can substitute sour cream or plain regular yogurt for Greek yogurt. These options will still provide moisture and a slight tanginess.

→ How do I store the muffins?

Store the muffins in an airtight container at room temperature for up to 2 days or in the refrigerator for up to a week. Reheat slightly to restore the freshness.

→ Can I make the batter ahead of time?

It’s best to assemble and bake the muffins immediately after preparing the batter to ensure proper rising and texture. However, the streusel topping and cream cheese filling can be made ahead and stored separately.

→ What can I use instead of the glaze?

If you prefer not to use glaze, you can sprinkle some powdered sugar over the cooled muffins for a simple finishing touch.

Moist Berry Cream Cheese Delight

Moist muffins with berries, creamy filling, and streusel topping.

Prep Time
15 Minutes
Cook Time
30 Minutes
Total Time
45 Minutes
By: Barbara


Difficulty: Intermediate

Cuisine: American

Yield: 10 Servings (10 muffins)

Dietary: Vegetarian

Ingredients

→ Streusel Crumb Topping

01 2/3 cup all-purpose flour
02 1/3 cup light brown sugar
03 1/4 teaspoon salt
04 1/4 cup unsalted butter, melted

→ Cream Cheese Filling

05 6 oz. cream cheese, room temperature
06 3 tablespoons granulated sugar
07 1 teaspoon vanilla extract
08 1 teaspoon cornstarch

→ Berry Muffins

09 1 cup all-purpose flour
10 1/4 teaspoon salt
11 1 teaspoon baking powder
12 1/4 cup vegetable oil
13 1/2 cup granulated sugar
14 1 large egg
15 1/2 teaspoon vanilla extract
16 1/2 cup Greek yogurt
17 1 1/2 cups fresh berries (1 cup blueberries and 1/2 cup raspberries)

→ Glaze

18 3/4 cup powdered sugar
19 1 1/2–2 1/2 teaspoons milk or cream

Instructions

Step 01

Preheat the oven to 425°F (220°C). Line a cupcake pan with paper liners and set aside.

Step 02

In a bowl, stir together flour, sugar, and salt. Add melted butter and mix with a fork until coarse crumbs form. Set aside.

Step 03

Mix softened cream cheese, sugar, cornstarch, and vanilla extract until just combined.

Step 04

In a large bowl, combine flour, baking powder, and salt, then set aside. In a medium bowl, whisk together egg and granulated sugar until combined. Mix in Greek yogurt, oil, and vanilla extract until the mixture turns pale yellow. Fold the wet ingredients into the dry ingredients, mixing until well combined. Gently fold in 1/2 cup of blueberries and 1/2 of the raspberries, ensuring the batter does not turn pink. Reserve remaining berries for topping.

Step 05

Spoon about 1 1/2 tablespoons of muffin batter into each cup. Spread the batter to create a small dent in the center, then add approximately 1 tablespoon of cream cheese filling to the center. Sprinkle a few berries on top and fill each cup to about 2/3 full. Top generously with streusel crumbs, pressing gently to adhere. Add a few additional berries on top if desired.

Step 06

Place the muffins in the preheated oven and reduce the temperature to 350°F (175°C). Bake for 30-35 minutes, or until the tops turn golden brown and the centers are set.

Step 07

Cool the muffins in the pan for 5-10 minutes, then transfer them to a rack to cool completely. To make the glaze, mix powdered sugar with milk or cream, starting with 1 teaspoon of liquid and gradually adding more until the desired consistency is achieved. Drizzle the glaze over each muffin before serving.

Notes

  1. Handle the batter gently when adding raspberries to avoid discoloring the mix.

Tools You'll Need

  • Cupcake baking pan
  • Paper liners
  • Mixing bowls
  • Fork
  • Rubber spatula
  • Cooling rack

Allergy Information

Please check ingredients for potential allergens and consult a health professional if in doubt.
  • Contains dairy (cream cheese and yogurt)
  • Contains gluten (flour)

Nutrition Facts (Per Serving)

It is important to consider this information as approximate and not to use it as definitive health advice.
  • Calories: 210
  • Total Fat: 8 g
  • Total Carbohydrate: 35 g
  • Protein: 4 g