Chock full of blueberries and a tangy cream cheese filling, homemade blueberry cream cheese muffins are a delightful addition to your breakfast or brunch.

Recipe Overview

Why you’ll love it: Once you begin making homemade muffins, you’ll never go back to bakery muffins. They are easy to make and taste so much better.

How long it takes: 33 minutes
Equipment you’ll need: muffin tins, mixing bowls
Servings: 12 muffins

Blueberry cream cheese muffin on top of other muffins.
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These blueberry muffins are amazing. They will definitely be added to the regular rotation here in our household. They have all the great taste of blueberry pancakes (my daughter E’s favorite), but you don’t need a fork to eat these gems.

And even better, there is a little pearl of cream cheese filling waiting for you in the middle of each one. It’s the icing on the cake, er, rather the filling in the cake. It’s flavorful and also makes the muffins a slightly more filling and hearty breakfast. It even adds a bit of healthy protein.

About This Muffin Recipe

These muffins are made with two types of flour: all-purpose white flour and whole wheat flour. Whole wheat makes a grainier muffin that is more nutritious but can be a little heavy and dense. Mixing it with all-purpose flour lightens the muffins up, making them fluffier and more like a delicious buttermilk pancake.

If you really love whole grain products, make the muffins with 100% whole wheat flour, or try these blueberry bran muffins with whole wheat flour and wheat bran. Whole wheat banana bread and whole wheat chocolate chip cookies (with oats!) are staples at my house and make great lunchbox treats.

Overhead view of muffin with scattered fresh blueberries.

Ingredient Notes

  • Whole Wheat Flour and All-Purpose Flour: If you prefer, just use one or the other.
  • Sugar: Granulated white sugar is added to the batter and to the filling.
  • Baking Powder, Salt: Normal muffin ingredients, the baking powder causes the muffins to rise and salt keeps them from tasting flat.
  • Eggs: Just a couple of treasures from the hen keeps the muffins moist and flavorful.
  • Buttermilk: Buttermilk has a nice tangy flavor that really goes well in the muffins. Think of buttermilk pancakes. Lowfat buttermilk is fine.
  • Canola or Vegetable Oil: Any mild tasting oil you happen to have is fine.
  • Blueberries (Fresh or Frozen): Both fresh blueberries and frozen blueberries work well. Don’t thaw frozen blueberries because the juice tends to make the muffin batter turn purple.
  • Cream Cheese: Use either full fat or reduced fat cream cheese. Make sure it is at room temperature so it’s soft enough to blend.
  • Vanilla: Pure vanilla extract is added to both the batter and the filling.
Ingredients needed in separate containers.

How To Make Blueberry Muffins

Get ready. Turn your oven on to preheat and prepare the muffin tins. This recipe makes 12 muffins. You can either spray the tins lightly with nonstick spray, grease them with shortening, or use paper mufffin liners.

Make the cream cheese filling. It’s important to have the filling ready before you make the muffin batter. Once you mix the batter, you want to get the muffins in the oven as soon as you can because the baking powder instantly reacts with the liquid and starts producing those little bubbles which make the muffins rise.

Blend the softened cream cheese with a fourth cup sugar and a teaspoon of vanilla extract. The cream cheese mixture should be smooth and creamy. If it seems a bit lumpy, beat it with your electric mixer a minute.

Cream cheese mixture and an electric mixer.

Mix wet ingredients. In a large bowl, whisk the two eggs. Add the oil, buttermilk, and vanilla extract, and then stir in the sugar.

Wet ingredients in mixing bowl with whisk.

Add dry ingredients. Add the flour, baking powder, and salt, lightly blending the dry ingredients together before stirring them into the egg mixture.

Dry ingredients being mixed before stirring into wet ingredients.

Don’t over mix the batter. It may be a little lumpy but that’s okay.

Muffin batter in a clear glass bowl.

Fold in blueberries. Use a gentle hand, so you don’t smoosh the berries.

Blueberries folded into batter.

Fill muffin cups. Spoon batter into each muffin cup (about ⅓ full). Next, drop a spoonful of the filling in the center of each muffin; then fill the muffin cups up with remaining batter.

Two images showing muffins being filled.

Bake. Bake the muffins until they are golden brown and firm to the touch. Let muffins cool in the tins for 5 to 10 minutes before removing them. Cool on a wire rack until ready to serve.

Blueberry muffins in muffin tin.


How can I make my muffins lighter and fluffy?

Using vegetable or canola oil instead of butter is one trick in the baker’s bag. Another trick is to very gently fold the dry ingredients into the egg mixture, without over mixing. If your muffins are still heavy, perhaps you added too many goodies, such as fruit, nuts, or chocolate chips, or used too much whole wheat flour.

Why did the blueberries sink in my muffins?

Because blueberries are heavy, they tend to sink. Some cooks recommend tossing the blueberries with a bit of flour before adding them to the batter but I haven’t found that technique to be particularly helpful.
Try filling the tins one third full with plain batter, then mixing the blueberries into the remaining batter.
However, I did find that the cream cheese filling in this recipe does seem to prevent the blueberries from sinking!

Do you need to cut blueberries for muffins?

Usually blueberries are the perfect size for muffins and don’t need to be cut. I have seen some really ginormous berries at the market lately and perhaps it would be wise to cut them in half (or don’t use that type for muffins!).

Recipe Variations

  • Substitute a different berry. Chopped strawberries, blackberries or raspberries, or cherries are good choices.
  • Lemon cream cheese filled muffins. For an easy variation, fill the muffins with a lemon cream cheese filling. The instructions are on the recipe card below.
  • Muffins with no filling. If you don’t care for cream cheese, or don’t want to hassle with a filling, simply omit the filling and bake as directed.
  • Add a streusel. Like muffins with crumb topping? For a good streusel recipe, use the same streusel featured in these whole wheat banana muffins with streusel.
  • Not a fan of berries? Try carrot cake muffins with cream cheese filling.
Muffin held in a hand.

Storage Tips

Blueberry cream cheese muffins can be stored at room temperature for a day but refrigerate for longer storage. They can be frozen for up to three months. Thaw them before serving.

More Blueberry Recipes

I just love Michigan blueberries and I have lots more blueberry recipes for you. Try:

More Muffin Recipes


Blueberry Cream Cheese Muffins

5 from 2 votes
Prep: 15 minutes
Cook: 18 minutes
Total: 33 minutes
Servings: 12 muffins
Chock full of blueberries and a tangy cream cheese filling, homemade blueberry cream cheese muffins are a delightful addition to your breakfast or brunch.
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Cream Cheese Filling

Muffin Batter

  • 2 large eggs
  • 1 cup buttermilk
  • ½ cup canola or vegetable oil
  • 1 teaspoon pure vanilla extract
  • ½ cup granulated sugar
  • 1 cup whole wheat flour
  • 1 cup all-purpose flour
  • 2 teaspoons baking powder
  • ½ teaspoon salt
  • 1 cup blueberries, fresh or frozen (unthawed)


  • Preheat oven to 400°F. Lightly spray a muffin tin with nonstick cooking spray.
  • In a small bowl, blend together softened cream cheese, sugar, and vanilla until smooth; set aside.
  • In a large mixing bowl, whisk together eggs, buttermilk, oil, and vanilla. Stir in sugar.
  • Add whole wheat flour, all-purpose flour, baking powder, and salt. Stir lightly just to mix dry ingredients and then stir the dry ingredients into the egg mixture just until combined. Do not overmix.
  • Gently fold in blueberries.
  • Fill muffin tins about ⅓ full with muffin batter. Using a small spoon, drop a small amount (rounded tablespoon) of the cream cheese mixture into each muffin cup on top of the batter. Top each muffin with remaining muffin batter.
  • Bake for 18 minutes or until golden brown. Cool 10 minutes in muffin tins before removing.


  • Yield may vary depending on the size of your muffin tins (or if you happen to throw in a few extra blueberries!). 
  • Muffins can be kept at room temperature for a day but for longer storage, store in an airtight container in the fridge.
  • If you prefer, omit whole wheat flour and substitute additional all purpose flour. 
  • Variation: Make lemon cream cheese filling. Substitute 1 teaspoon lemon juice for the vanilla extract and stir in 1 teaspoon finely grated lemon zest.



Serving: 1muffin, Calories: 172kcal, Carbohydrates: 32g, Protein: 7g, Fat: 2g, Saturated Fat: 1g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 1g, Trans Fat: 1g, Cholesterol: 32mg, Sodium: 332mg, Potassium: 148mg, Fiber: 2g, Sugar: 16g, Vitamin A: 90IU, Vitamin C: 1mg, Calcium: 139mg, Iron: 1mg

Nutrition information is automatically calculated, so should only be used as an approximation.

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5 from 2 votes (2 ratings without comment)

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  1. Stephanie @ Eat. Drink. Love. says:

    I love everything about these, but especially the cream cheese filling!

  2. sarah k @ the pajama chef says:

    i’ve never tried pancake muffins but they look so fun! love that filling too. yum!