There’s something magical about biting into a muffin and discovering a creamy, cheesecake-filled center surrounded by soft, chocolate-studded cake. Cheesecake Chocolate Chip Muffins bring the best of both worlds together—rich, tangy cream cheese paired with a moist, tender muffin. Perfect for breakfast, dessert, or an afternoon treat, these muffins are surprisingly simple to make at home. You don’t need fancy equipment or advanced baking skills. Just follow along, and you’ll be baking like a pro in no time.

Why You’ll Love This Cheesecake Chocolate Chip Muffins Recipe

This isn’t your ordinary muffin recipe. With a luscious cheesecake filling and plenty of melty chocolate chips, these muffins are indulgent yet approachable for any home baker. Here’s why they deserve a spot in your baking rotation:

Key Benefits

They’re easy enough for beginners. You don’t need any special techniques—if you can stir and scoop, you’re set.

Bakery-quality results. These muffins rise beautifully with golden domes and soft, tender crumbs that rival your favorite coffee shop.

Perfect for any occasion. Whether you’re making a batch for a weekend brunch, packing them in lunchboxes, or impressing guests at a bake sale, they fit right in.

Customizable to your taste. Swap chocolate chips for white chocolate or add a handful of chopped nuts for texture. You can even turn them into mini muffins for bite-sized treats.

Suitable For

This recipe is ideal for anyone looking for an impressive yet fuss-free bake. It’s great for families—kids love the surprise cheesecake center—and works equally well as a cozy baking project on a rainy afternoon. Even if you’ve never baked muffins before, you’ll feel confident tackling this recipe.

Ingredients for Cheesecake Chocolate Chip Muffins

The beauty of these muffins lies in their simple, pantry-friendly ingredients. Here’s what you’ll need and why each plays an important role.

Core Ingredients

• All-purpose flour (2 cups): Provides structure and a tender crumb.

• Granulated sugar (½ cup) and brown sugar (¼ cup): A mix of sugars balances sweetness and adds a hint of molasses richness.

• Baking powder (1 tablespoon): Gives the muffins their beautiful rise.

• Salt (½ teaspoon): Enhances flavors and balances the sweetness.

• Whole milk (¾ cup): Keeps the batter moist and tender.

• Unsalted butter (½ cup, melted): Adds richness and helps create a soft, fluffy texture.

• Eggs (2 large): Bind everything together and provide structure.

• Vanilla extract (1 teaspoon): Brings warm, aromatic notes to both the batter and the filling.

• Semi-sweet chocolate chips (1 cup): Chocolatey pockets in every bite.

For the cheesecake filling:

• Cream cheese (8 ounces, softened): The star of the filling—smooth, rich, and tangy.

• Granulated sugar (¼ cup): Sweetens the filling just enough.

• Egg yolk (1 large): Helps set the cheesecake layer so it’s creamy, not runny.

• Vanilla extract (1 teaspoon): Adds depth and complements the tangy cream cheese.

Substitutions and Tips

Dairy-free? Use plant-based milk and a vegan butter substitute. Choose a dairy-free cream cheese for the filling.

No chocolate chips? Try chopped dark chocolate, white chocolate chunks, or even dried fruit for a different twist.

Want richer muffins? Swap half of the milk for sour cream or yogurt for extra moisture and flavor.

Pro tip: Always use room temperature cream cheese for the filling. Cold cream cheese will lead to lumps no matter how much you mix.

The Best Cream Cheese and Chocolate Chips for Muffins

Cream Cheese Matters

Go for full-fat cream cheese blocks, not the whipped or spreadable kind. The block form has the perfect consistency for a rich, creamy filling that stays put as the muffins bake.

Choosing Chocolate Chips

Semi-sweet chocolate chips strike the perfect balance between sweet and rich. Mini chocolate chips distribute more evenly throughout the batter, while larger chunks give you big, molten bites of chocolate. Both work beautifully, so use what you love.

Kitchen Tools You’ll Need

You don’t need a professional kitchen to bake these muffins, but a few basic tools will make the process smoother.

Must-Have Tools

• 12-cup muffin tin: The classic size for perfectly portioned muffins.

• Mixing bowls (large and medium): One for the muffin batter, one for the cheesecake filling.

• Whisk and spatula: For mixing wet and dry ingredients without overworking the batter.

• Hand mixer or stand mixer: Useful for beating the cheesecake filling to silky smoothness.

Nice-to-Have Tools

• Ice cream scoop or large cookie scoop: Makes portioning batter a breeze and ensures even layers.

• Parchment muffin liners: Prevents sticking and makes cleanup easier.

How to Make Cheesecake Chocolate Chip Muffins: Step-by-Step Guide

Now that you’re all set with ingredients and tools, let’s dive into the fun part—bringing these decadent muffins to life. You’ll be amazed at how simple each step is, and by the end, your kitchen will smell like a cozy bakery.

Step 1: Preheat and Prep

Start by preheating your oven to 375°F (190°C). This ensures the oven is hot enough to give your muffins a beautiful rise right from the start.

Line a 12-cup muffin tin with paper liners or grease each cup well with butter or cooking spray. If you love tall, bakery-style muffin tops, use parchment paper liners that stick up above the rim of the tin.

Step 2: Make the Cheesecake Filling

In a medium mixing bowl, beat together the softened cream cheese, granulated sugar, egg yolk, and vanilla extract. Use a hand mixer on medium speed until the mixture is silky smooth and lump-free.

Pro tip: If your cream cheese isn’t fully softened, cut it into cubes and microwave for 10-15 seconds. You want it soft but not melted.

Set this filling aside while you prepare the muffin batter.

Step 3: Prepare the Muffin Batter

In a large bowl, whisk together the all-purpose flour, granulated sugar, brown sugar, baking powder, and salt. These dry ingredients form the structure of your muffins.

In another bowl, combine the whole milk, melted butter, eggs, and vanilla extract. Whisk until smooth.

Pour the wet ingredients into the dry ingredients and gently stir with a spatula or wooden spoon. Stop mixing as soon as the flour streaks disappear. Overmixing can lead to dense muffins instead of the tender, airy texture we’re after.

Fold in the chocolate chips, saving a small handful to sprinkle on top later if you like.

Step 4: Assemble the Muffins

Scoop about 2 tablespoons of muffin batter into the bottom of each muffin cup.

Add 1 tablespoon of cheesecake filling to the center of each cup, gently spreading it a bit but not all the way to the edges.

Top with another 2 tablespoons of muffin batter, covering the cheesecake layer completely. If you held back a few chocolate chips, sprinkle them on now for that irresistible chocolate-studded top.

Step 5: Bake and Cool

Place the muffin tin in the preheated oven and bake for 18 to 22 minutes. Check for doneness by inserting a toothpick into the muffin (avoiding the cheesecake center). If it comes out clean or with a few moist crumbs, they’re ready.

Allow the muffins to cool in the pan for 5 minutes. Then transfer them to a wire rack to cool completely. This prevents the bottoms from becoming soggy.

Tips for Success

• Don’t overfill the muffin cups. Stick to about three-quarters full to avoid overflowing.

• Room temperature ingredients are key. They mix more evenly and create a smoother batter and filling.

• For extra flavor, add a pinch of cinnamon or espresso powder to the muffin batter for a subtle twist.

• Use an ice cream scoop to portion batter for consistent muffin sizes and even baking.

How to Store Cheesecake Chocolate Chip Muffins

At Room Temperature

Store muffins in an airtight container for up to two days. Keep them in a cool, dry spot out of direct sunlight.

In the Refrigerator

Since these have a cream cheese filling, they’ll keep best in the fridge for up to five days. Place them in an airtight container, and bring them to room temperature or warm slightly before serving.

Freezing Tips

Wrap each muffin individually in plastic wrap and place them in a freezer-safe bag or container. They’ll stay fresh for up to three months. To enjoy, thaw overnight in the fridge and warm in the oven or microwave.

Frequently Asked Questions

Can I use low-fat cream cheese?

Yes, but the filling won’t be as rich and creamy. Full-fat cream cheese gives the best texture and flavor.

Why did my muffins sink in the middle?

This usually happens if the batter is overmixed or the oven temperature fluctuated. Next time, mix gently and use an oven thermometer to ensure accuracy.

Can I make these gluten-free?

Absolutely. Substitute a high-quality 1:1 gluten-free baking flour blend for the all-purpose flour.

Can I turn these into mini muffins?

Yes. Use a mini muffin tin and reduce the baking time to about 10-12 minutes. Keep an eye on them since they bake quickly.

Related Recipes You’ll Love

If you loved these Cheesecake Chocolate Chip Muffins, you might enjoy these other sweet treats:

• Lemon Raspberry Cupcakes: Bright, fruity, and perfect for spring.

• Chocolate Peanut Butter Cake: A rich, decadent combo of chocolate and peanut butter.

• Pineapple Upside Down Cupcakes: A fun twist on a classic dessert.

Conclusion

Cheesecake Chocolate Chip Muffins are proof that a little extra effort in the kitchen pays off big time. With a creamy, tangy surprise inside and plenty of chocolate in every bite, these muffins are guaranteed to become a family favorite. Bake a batch, share them with loved ones, and watch them disappear.

Want to level up your baking? Try experimenting with mix-ins or turn them into a holiday treat with peppermint chips or a swirl of raspberry jam. The possibilities are endless.

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