You have just found your new favorite crowd-wowing recipe – triple berry cheesecake muffins! Packed with fresh berries, these moist, fluffy muffins are layered with cheesecake goodness. Plus, I’m teaching you my tried and true steps to making impressive bakery-style domed tops! 

rows of triple berry cheesecake muffins on a light pink surface, some sitting upright, some on their sides, some cut in half and some with a bite out

The Absolute Best Triple Berry Cheesecake Muffins Recipe

Cheesecake meets muffin mixed with fresh berries. A match made in dessert heaven and the perfect addition to my muffin recipes collection! I dedicated six months in my kitchen to testing and perfecting the perfect muffins, all so I could provide you with an easy step-by-step guide to the best muffins made at home! 

No baking experience required, and you can make these triple berry muffins with rich cheesecake layers in just 10 minutes of prep! I use fresh blueberries, raspberries, and blackberries, but you can easily customize these with whatever your favorite berries are or what you happen to have on hand. 

Keep reading for all my best muffin tips and tricks to easily master homemade muffins!  

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a triple berry cheesecake muffin sitting on a light pink surface with its muffin liner partially peeled away, surrounded by fresh blueberries, blackberries and raspberries

Why You’ll Love These Triple Berry Cheesecake Muffins

There are so many things to love about these berry cheesecake muffins, but here are a few of my favorite things:

  • Everyday ingredients, prepped in 10 minutes
  • Packed with berry flavor from three types of juicy berries
  • Customizable with your favorite berries
  • Great for snacks, desserts, or late-night snacks!
  • Moist, soft muffins with tender crumb
  • Tall and domed muffin tops (bakery style!)
a triple berry cheesecake muffin missing one bite that exposes it's center, laying on its open muffin liner with raspberries, blackberries and blueberries around it, on top of a muffin pan full of more muffins

What You’ll Need for Triple Berry Cheesecake Muffins

These mixed berry cream cheese muffins are made from basic ingredients; even the cheesecake layer only has 4 simple ingredients! Get the full recipe with measurements and instructions in the recipe card below. Here’s what you’ll need:

Cream Cheese Layer

  • Cream cheese: leave time to let the cream cheese get to room temperature
  • Egg yolk
  • Granulated sugar
  • Vanilla extract

Muffins

  • All-purpose flour
  • Granulated sugar
  • Baking powder
  • Salt
  • Ground nutmeg or cinnamon
  • Eggs
  • Buttermilk
  • Vegetable oil
  • Vanilla extract
  • Fresh berries: I used raspberries, blueberries, and blackberries.
a clear glass bowl of triple berry cheesecake muffin batter sitting on a light pink surface

How to Make Triple Berry Cheesecake Muffins

While it looks impressive, this easy recipe has just 7 simple steps. Get the full recipe with measurements and ingredients in the recipe card below. Here are the step-by-step instructions for making triple berry cheesecake muffins:

  1. Rest time. This recipe requires a 30 minute rest before baking. This is an important step because of the excess liquid from the fresh fruit.

Cream Cheese Layer

  1. Make cheesecake filling. Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins. 

Muffins

  1. Mix dry ingredients. In a mixing bowl combine the flour, granulated sugar, baking powder, salt, and nutmeg. Stir together and set aside.
  2. Mix wet ingredients. In a large mixing bowl combine the eggs, buttermilk, vegetable oil, and vanilla extract. Stir to combine with a spatula.
  3. Combine wet and dry ingredients. Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. Gently mix in the fresh berries.
  4. Rest muffin batter. Cover the bowl with a towel and allow the batter to rest for 30 minutes. Preheat the oven to 425ºF / 220ºC.
  1. Line and fill muffin pans. For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. Fill the liners with 2 tablespoons of batter. Drop ½ tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops with sanding sugar.
  1. Refrigerate batter and rotate baking. While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.
a stack of 3 triple berry cheesecake muffins sitting on a pink surface, surrounded by fresh blueberries, blackberries and raspberries

How to Create Bakery Style Muffins

Bakery style muffins are known for their domed tops. Plus who doesn’t love them? I used a few techniques to help “lift” these muffins so they would have large, domed tops!

1. THE REST PERIOD

Let the batter rest for 15 minutes after it’s mixed and before you scoop it into the muffin pan. During the resting period, starch molecules in the flour are absorbing the liquid in the batter, causing them to swell and giving the batter a thicker consistency (ref the kitchen whisper). Our 15 minute rest is just a quick rest. 

2. FILL EVERY OTHER MUFFIN CUP

This tip has been a game changer! For bakery style muffin tops, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. Filling every other cup allows the muffins to spread and dome without running into each other. This technique also encourages the muffins to brown, creating a golden muffin top.

3. FILL THEM TO THE TOP

Fill your muffin liners to the top with batter. Yes, this goes against everything you’re heard but it’s important in helping the muffin gain that height.

4. BAKE AT HIGH TEMPERATURE INITIALLY

Bake the muffins at a high temperature (425ºF) initially, then lower to 350ºF. Starting the muffins off at a higher temperature causes the batter to rise rapidly, setting the outer surface of the muffin, producing a dome shape.

How to Properly Measure Flour

The most accurate way to measure flour is to use a kitchen scale, weighing it in grams. 

If you don’t have a kitchen scale, follow this method. 

  • Aerate the flour with a whisk or spoon. Flour becomes heavy and compact as it sits. Aerating is the same as fluffing the flour, but not the same as sifting it. Do not sift the flour unless the recipe specifically calls for it.
  • Use a spoon to sprinkle the flour into the measuring cup. Do not tap the cup against the counter, as this will compact the flour.
  • Use the back of a butter knife to level off the excess.
a triple berry cheesecake muffin missing one bite that exposes it's center, laying on its open muffin liner with raspberries, blackberries and blueberries around it, on top of a muffin pan full of more muffins

Tips for the Best Triple Berry Cheesecake Muffins

Berry filled, moist muffins with a luscious cheesecake layer, it just can’t get any better. Here are a few tips to make the perfect muffin

  • Don’t skip rest time: Allow the batter to rest for 15 minutes in the mixing bowl.
  • Top the muffins with sanding sugar: For a true bakery style muffin, top them with a sprinkling of crunchy sparkling sugar.
  • Make bakery-style tall, domed muffin tops: Filling every other cup allows the muffins to spread and dome without running into each other. This technique also encourages the muffins to brown, creating a golden muffin top.
  • Start at a higher temp, then lower: Bake at a higher temperature initially to cause the muffins to rise quickly.
a triple berry cheesecake muffin sitting on a light pink surface surrounded by fresh blueberries, blackberries and raspberries

Substitutions & Variations

These golden brown muffins with a cheesecake-like center are always a huge hit! If you need to change them up a little, here are some options:

  • Swap fresh berries for frozen berries: You can use frozen mixed berries if you don’t have fresh available. Do not thaw them.
  • Make these gluten free: Simply substitute the flour. I recommend King Arthur’s Gluten Free Measure for Measure Flour. Use it as a one for one substitute for regular flour.
  • Make them more decadent: ​Adding white chocolate chips would add more sweetness to this recipe, making them perfect for Valentine’s Day.
  • Zest it up: Top with a bit of lemon zest to really brighten it up with fresh citrus flavor.

Storing and Freezing Muffins

MUFFIN STORAGE

If you’ll be eating the muffins within 24 hours of baking, you can leave them uncovered on the counter. The muffins will not dry out while left at room temperature for 1 day. 

In fact, muffins are so moist they can become soggy and those crunchy, sugary tops can disappear when stored in an airtight container.

But I have a trick to help that – paper towels. 

For longer storage, 2-4 days, line the bottom of an airtight container with paper towels. Place the muffins in a single layer in the container then cover the muffins with any additional layer of paper towels. The paper towels will act like a sponge, absorbing the moisture they release while they are stored. 

If the paper towels become too moist around day 2 or day 3, replace them with fresh paper towels. 

HOW TO FREEZE MUFFINS

Individually wrap each muffin in plastic wrap. Then place them in a ziploc bag or airtight container and place in the freezer for up to 3 months.

To thaw, leave them at room temperature until defrosted, about 1 hour. Or unwrap them and microwave at 20 second intervals until defrosted.

More Cheesecake Recipes

a triple berry cheesecake muffin missing one bite that exposes it's center, laying on its open muffin liner with raspberries, blackberries and blueberries around it, on top of a muffin pan full of more muffins

Triple Berry Cheesecake Muffin Recipe

5 from 2 ratings
Prep Time: 10 minutes
Cook Time: 24 minutes
Resting Time: 30 minutes
Yield: 10 muffins
You have just found your new favorite crowd-wowing recipe – triple berry cheesecake muffins! Packed with fresh berries, these moist, fluffy muffins are layered with cheesecake goodness. Plus, I’m teaching you my tried and true steps to making impressive bakery-style domed tops! 

Ingredients

Cream Cheese Layer

  • 8 oz cream cheese, room temperature, 227 grams
  • 1 egg yolk
  • ½ cup granulated sugar, 100 grams
  • 2 tsp vanilla extract

Muffins

  • 3 cups all-purpose flour, 360 grams
  • 1 ½ cups granulated sugar, 300 grams
  • 3 tsp baking powder
  • ½ tsp salt
  • ¼ tsp ground nutmeg or cinnamon
  • 2 large eggs
  • ¾ cup buttermilk, 180 ml
  • ½ cup vegetable oil, 118 ml
  • 2 tsp vanilla extract
  • 2 cups fresh berries, I used raspberries, blueberries and blackberries, 225 grams

Instructions
 

  • This recipe requires a 30 minute rest before baking. I recommend a 30 minute rest because of the excess liquid from the fresh fruit.

Cream Cheese Layer

  • Place the cream cheese, egg yolk, sugar, and vanilla extract in a mixing bowl and beat with an electric mixer for 1-2 minutes, until smooth. Place the bowl in the freezer while you prep the rest of the recipe. Chilling the filling will help keep it from melting into the muffins.

Muffins

  • In a mixing bowl combine the flour, granulated sugar, baking powder, salt, and nutmeg. Stir together and set aside.
  • In a large mixing bowl combine the eggs, buttermilk, vegetable oil, and vanilla extract. Stir to combine with a spatula.
  • Gradually mix the dry ingredients into the wet ingredients, mixing just until combined. Gently mix in the fresh berries.
  • Cover the bowl with a towel and allow the batter to rest for 30 minutes. Preheat the oven to 425ºF / 220ºC.
  • For bakery style muffins, line a 12 count muffin pan with 6 muffin liners, meaning you’ll only fill every other muffin well with batter. Fill the liners with 2 tablespoons of batter. Drop ½ tbsp of the cream cheese mixture into each muffin cup. Use a toothpick to swirl into the batter. Then add 6 tablespoons of batter, covering the cream cheese. Top each muffin with ½ tbsp of cream cheese, swirling with a toothpick. Sprinkle the tops with sanding sugar.
  • While one pan is baking, refrigerate the remaining batter in the bowl. Place one pan in the center of the oven and bake for 7 minutes at 425ºF / 220ºC, then keep the muffins in the oven, turn the temperature down to 350ºF / 180ºC and bake for 18-21 minutes or until a toothpick inserted in the center comes out clean. Allow the muffins to cool in the pan. Repeat with the remaining batter, bumping the temperature back up to 425ºF / 220ºC.

Notes

  • You can use frozen mixed berries, do not thaw them.
Cuisine: American
Course: Dessert
Author: Beth
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