Double Chocolate Cheesecake Muffins

Even though my mom loves to cook, growing up we didn’t make a lot of breakfast food. My sister wasn’t a fan of any of the breakfast meats, and I didn’t develop a taste for eggs until I was 20. Eliminating both the meat and egg options for breakfast didn’t leave us many options left. Most of the time I would just toast up a couple of Eggo waffles before school. However, whenever my family would go somewhere for the weekend, we would stop at Big Apple Bagels first. Of course, being a chocolate lover, instead of getting a bagel, I would always get a Jumbo Double Chocolate Cream Cheese Muffin instead. 

Now that I’m older, I recognize the value of a healthy breakfast, and I actually love fried eggs now that I’ve given them a chance. That doesn’t mean that I can’t appreciate a delicious muffin here or there though. Most of the time I stick to making pumpkin spice muffins or plain chocolate chip, but lately I’ve been craving double chocolate muffins with cheesecake filling. I had been practicing making cheesecakes for dessert the last couple of months, and I realized I could easily transform the cheesecake ingredients into a filling for my muffins. Making the regular chocolate chip muffins into double chocolate chip was also a simple fix, I simply added in cocoa powder and a little more milk to offset the extra powder that was now in it. 

After a couple of rounds of experimenting with this recipe, I am completely obsessed. These are so delicious! If I wasn’t trying to be health conscious, I would probably make them up all the time and eat two for breakfast every day. Instead, these will remain a special treat here and there, which will make me appreciate them a little more too.



2 ½ cups flour

1 tbsp Baking Powder

⅓ cup Cocoa Powder

1 tsp Salt

1 ⅓ cup Semi Sweet Chocolate Chips

½ cup (1 stick) Melted Butter

1 cup Sugar

1 ⅔ cup Whole Milk

2 Large Eggs

1 tbsp Vanilla

Cheesecake Filling

12 oz Cream Cheese

2 Egg Yolks

1 tsp Vanilla

6 tbsp Sugar


Like any baking recipe, the first step to making these muffins is to preheat your oven to 425 degrees, then you are going to start mixing your muffin batter together. When making the muffin batter, you are going to mix all of the dry ingredients except the sugar first. You are going to want a large mixing bowl for this. 

Pour the flour, baking powder, cocoa powder, and salt into the bowl. To switch things up a little, I like to divide my cocoa powder in half. I fill half of the ⅓ cup with regular cocoa powder, and then I fill it the rest of the way with dark chocolate cocoa powder. When eating chocolate, I almost always prefer dark chocolate options, and this sets these muffins apart from other double chocolate muffin recipes. 

After all the dry items are combined, add in chocolate chips to the bowl and whisk them in. 

Once all of your chocolate chips are added in, take out a new glass bowl (or microwave safe at least). You will want to make sure this bowl is large enough to both hold the rest of your ingredients and be able to whisk them together. Start out by melting the butter and cream it together with your sugar. Let this cool a little bit before adding in the rest of the ingredients. Once the butter/sugar mixture is at room temp, add in your milk, eggs, and vanilla and whisk it all together. 

When your liquids are well mixed together, you are going to add them into your dry ingredients. You will want to use a rubber spatula during this next step, and you will want to continuously scrape the bottom and sides of the bowl while folding the batter together. If you don’t scrape the sides and bottoms often enough you will still have dry ingredients left on the bottom of the bowl when you start scooping it into your muffin tins. After your batter is mixed together, set it aside and start working on your cheesecake filling

For the cheesecake filling you will want to use either a stand up or hand mixer. I like to take my cream cheese out of the fridge about an hour and a half before I make this recipe. This helps the cream cheese to soften and makes it easier to mix together. 

Start with the cream cheese and mix it until it looks smooth. It won’t get entirely smooth until the rest of the ingredients are added in, but you should be able to see a clear difference in the consistency after a little bit of mixing. 

After your cream cheese changes consistency, add in your egg yolks, vanilla, and sugar. When mixing these next items together, use a medium to high speed setting. This speed will allow the ingredients to get a very creamy texture.  You are going to need to pause every once in a while during this mixing process to scrape the sides and bottom of the bowl with a rubber spatula. If you don’t scrape the bowl, then some cream cheese will stick to it and create lumps later if they fall into your filling. Your filling is done when it is completely mixed together and looks yellowed and creamy. 

When both your batter and filling are finished, you need to prep your muffin pans. This recipe makes 24 muffins, so you will either need two muffin pans or have to bake it in batches. I like to use muffin tins to keep the pans easier to wash. I’ve never tried making them with just greasing the pans, but I’m guessing that would work too. 

Start to fill your pans by putting one scoop of muffin batter in the base of each cup. This first scoop should be ¼ of an inch to ½ thick once it is in the cup. I lean towards the side of a 1/2 inch to keep a more solid base. 

After you have a base in each tin, add in one spoon of cheesecake filling on top of it. Warning: If you put too much cheesecake filling in, these muffins will overflow a little bit. Most silverware sets have both small spoons and large spoons in them. I use the large spoons when making these muffins. I have found that one large spoonful of cheesecake filling is perfect, but one heaping spoonful will lead to a bit of a muffin explosion.

Finally, top off your cheesecake filling with another scoop of batter in each tin. Smooth the batter over the top so you can’t see the cheesecake filling anymore. Most muffin recipes will tell you only to fill each cup ⅔ of the way full, but I fill these all the way to the rim. Filling it all the way full creates a nice muffin top, and since there isn’t any baking soda in this recipe it doesn’t rise too much that this is an issue. 

Now your muffins are ready to go in the oven! You are only going to bake your muffins at 425 degrees for the first 5 minutes of the bake time. After the first 5 minutes it is essential that you turn your oven down to 350 degrees. Bake your muffins for another 16 minutes, and they will be finished.

Important Storage Information

Because these muffins have a cheesecake filling they have to be stored in the refrigerator. When you want to eat one, just peel off the muffin tin and heat it up in the microwave for 20 seconds. This will warm it up and allow the filling to get the gooey delicious texture that melts in your mouth. You can also freeze these muffins and thaw them out for future use since this recipe makes up quite a lot.

I hope these muffins provide you with many delicious breakfasts in the future! Enjoy!

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