Blueberry Cheesecake Muffins

The blueberry muffins that finally beat out your favorite bakery’s version.

These Blueberry Cheesecake Muffins are a fresh way to brighten up your weekend breakfast situation. Everyone loves a good blueberry muffin and these muffins are literally a step above regular blueberry muffins. Breakfast and Brunch just got leveled up!

Twelve Blueberry Cheesecake Muffins with crumb topping cool on a wire rack, surrounded by a few loose blueberries and a yellow-striped kitchen towel.

The flavor of these Blueberry cheesecake muffins is like a sweet, soft blueberry muffin crossed with your favorite cheesecake. The layers of soft muffin, fresh blueberries, tangy cream cheese and a little crumb topping work wonders to make these muffins quite possibly the best muffins you’ll ever bake at home. Everything you love in one crumbly bite.

Several Blueberry Cheesecake Muffins with crumb topping are arranged on a cooling rack.

Weekend Wows!

These are just right for brunches, lazy weekend mornings, or any time you want to make breakfast feel extra special. They’re great for serving guests or just treating yourself to something homemade and warm from the oven.

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I just think blueberries might be my favorite breakfast berry. We love blueberry danishes with hot coffee or this easy blueberry coffee cake is also amazing.

A top-down view of baking ingredients in bowls, perfect for Blueberry Cheesecake Muffins, including Greek yogurt, eggs, blueberries, flour, milk, baking powder, salt, vanilla extract, sugar, and melted butter.

Ingredients For Blueberry Cheesecake Muffins

Make sure you have everything on hand before you start. These muffins come together quickly once you begin mixing so check your fridge and pantry for fresh blueberries cream cheese and Greek yogurt to be ready to bake without delay.

  • melted butter
  • granulated sugar
  • large eggs
  • vanilla extract
  • Greek yogurt
  • milk
  • salt
  • all-purpose flour
  • fresh blueberries
  • baking powder
  • cream cheese
  • brown sugar
  • muffin tins
  • muffin papers (optional, you can just grease the muffin pan)

If you want to change it up, add a little lemon zest to the batter for a bright citrus touch. Swap in raspberries or chopped strawberries for a different berry flavor.

Add nuts to the top of the muffin batter before baking. Chopped pecans, walnuts or even slivered almonds work really well on top of muffins.

Tips To Make The Best Muffins

Fruit has a tendency to sink when you add it to baked goods. Tossing the fresh fruit with a little flour can help the fruit stay put and not sink. Is it perfect? No, but it does help. Just be sure not to over flour it, just toss it lightly with a Tablespoon of flour.

Don’t over mix the batter, the worst thing you can do is beat quick bread batter instead of stirring it. You don’t want to develop the gluten, some lumps in the batter are just fine.

One more tip is to measure carefully. Make sure your flour is gently loosened by running a spoon through it and THEN measure it out. This will keep you from adding too much flour.

A close-up of Blueberry Cheesecake Muffins with crumb topping, showing a cross-section filled with creamy cheesecake and visible blueberries inside.

To Store These Muffins

Leftovers can be stored in an airtight container at room temperature for a day or two, or in the fridge for up to four days. Reheat briefly in the microwave to enjoy warm again.

A close-up of Blueberry Cheesecake Muffins cut in half, showing a creamy filling and blueberries inside, with a crumbly topping, resting on a muffin liner.
Blueberry Cheesecake Muffins with crumb topping in paper liners are cooling on a wire rack, with a yellow striped cloth and loose blueberries in the background.

Blueberry Cheesecake Muffins

5 from 1 vote
The blueberry muffins that finally beat out your favorite bakery’s version.
Course: Breakfast
Cuisine: American
Prep Time: 15 minutes
Cook Time: 25 minutes
Total Time: 40 minutes
Servings: 12 Muffins
Calories: 385kcal
Author: Laura
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Ingredients

Muffin Batter

  • ½ cup unsalted butter melted
  • 1 cup granulated sugar
  • 2 large eggs
  • 1 tsp vanilla extract
  • cup Greek yogurt
  • ½ cup milk
  • ¼ tsp salt
  • 2 cup all-purpose flour plus 1 tbsp for coating blueberries
  • 2 cup fresh blueberries
  • 2 tsp baking powder

Cream Cheese Filling

  • 6 oz cream cheese softened
  • 2 tbsp granulated sugar
  • 1 tsp vanilla extract
  • 1 tsp milk
  • 1 tsp all-purpose flour

Crumble Topping

  • ¼ cup unsalted butter melted
  • cup brown sugar
  • cup all-purpose flour

Instructions

  • Preheat oven to 350°F (175°C)
  • Line a 12-cup muffin tin with paper liners

Make the batter

  • Toss 1½ cup blueberries with 1 tbsp flour and set aside
    A glass bowl filled with blueberries coated in a layer of white flour, photographed from above on a white background—perfectly prepped for Blueberry Cheesecake Muffins.
  • Reserve remaining ½ cup blueberries for topping
  • In a large bowl, mix melted butter and sugar until smooth
    A glass mixing bowl containing melted butter and sugar, the perfect start for baking delicious Blueberry Cheesecake Muffins, sits on a white background.
  • Add eggs and mix until combined
    A clear glass mixing bowl containing two raw eggs and melted butter on a white background, perfect for starting your Blueberry Cheesecake Muffins recipe.
  • Add vanilla, yogurt, and milk; mix again
    A glass mixing bowl containing milk, melted butter, yogurt, spices, and ingredients for Blueberry Cheesecake Muffins sits on a white surface.
  • In a separate bowl, whisk flour, baking powder, and salt
    A glass bowl filled with white flour, viewed from above on a white background—perfect for creating delicious Blueberry Cheesecake Muffins.
  • Add dry ingredients to wet and stir until just combined
    A glass mixing bowl containing a pale, creamy batter for Blueberry Cheesecake Muffins, with patches of unmixed flour on the surface, set against a white background.
  • Fold in flour-coated blueberries and set aside
    A glass mixing bowl with batter and flour-coated blueberries being stirred for Blueberry Cheesecake Muffins using a wooden spatula on a white background.

Make the cream cheese filling

  • In a bowl, beat cream cheese, sugar, vanilla, milk, and flour until smooth
    A glass mixing bowl containing whipped cream cheese on a white surface, perfect for making Blueberry Cheesecake Muffins.
  • Transfer to a piping bag or zip-top bag with the corner snipped off
    A clear plastic piping bag filled with white icing or cream, perfect for topping fresh blueberry cheesecake muffins, placed on a white surface.

Make the crumble

  • Mix brown sugar and flour
    A glass bowl contains a mixture of flour and other dry ingredients for Blueberry Cheesecake Muffins, being stirred with a metal fork with a dark wooden handle.
  • Add melted butter and stir until crumbly
    A glass bowl filled with a crumbly brown sugar and flour mixture, perfect for topping Blueberry Cheesecake Muffins, with a fork resting inside, on a white background.

Assemble the muffins

  • Fill each muffin liner ⅔ full with batter
    A muffin tin with twelve paper liners filled with raw Blueberry Cheesecake Muffins batter, ready to be baked.
  • Pipe 1 tbsp cream cheese filling into the center of each muffin
    A muffin tray with twelve paper liners filled with unbaked Blueberry Cheesecake Muffins batter and a generous streusel topping.
  • Top with remaining blueberries and a sprinkle of crumble
    A muffin tin with twelve Blueberry Cheesecake Muffins, each topped with crumbly streusel and some showing juicy blueberries peeking through.

Bake

  • Bake for 23–25 minutes, until tops are golden and a toothpick inserted at the edge comes out clean
  • Let cool in the pan for 5 minutes, then transfer to a wire rack
  • Serve warm if desired
    Several Blueberry Cheesecake Muffins with crumb topping are arranged on a cooling rack.

Video

Notes

  • Coating the blueberries in flour helps prevent sinking during baking.

Nutrition

Serving: 1 Serving | Calories: 385kcal | Carbohydrates: 51g | Protein: 6g | Fat: 18g | Saturated Fat: 11g | Polyunsaturated Fat: 1g | Monounsaturated Fat: 5g | Trans Fat: 0.5g | Cholesterol: 74mg | Sodium: 184mg | Potassium: 114mg | Fiber: 1g | Sugar: 28g | Vitamin A: 615IU | Vitamin C: 2mg | Calcium: 91mg | Iron: 2mg

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One Comment

  1. 5 stars
    The recipe was easy to follow and very delicious. I added lemon rind to the batter and cream cheese which brought out the taste of the blueberries. Hadn’t baked muffins in over ten years due to a disability, the family was very happy I chose this one for the first.
    Thanks, we appreciate it.

5 from 1 vote

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