These Lemon Cream Cheese Muffins are the perfect balance of tangy and sweet, combining fresh lemon zest and juice with a creamy swirl of cream cheese.
A delicious treat for breakfast, brunch, or dessert, they’re easy to prepare and offer a burst of flavor in every bite.
With a hint of kefir for extra moisture and protein, these muffins are a delightful way to satisfy your cravings while keeping it simple.

Lemon Cream Cheese Muffins
Equipment
- 1 Muffin pan (12-cup) with liners or lightly greased
- 2 mixing bowls
- 1 Measuring Spoons Set
- 1 kitchen scale
- 1 whisk
- 1 spatula
- 1 Hand mixer (recommended for cream cheese mixture)
- 1 Wire Cooling Rack
Ingredients
- 250 g 2 cups all-purpose flour
- 1 tsp baking soda
- 1 tsp baking powder
- ½ tsp salt
- 200 g 1 cup granulated sugar
- 2 tbsp lemon zest
- 170.1 g 6 oz cream cheese, softened
- 1 tbsp lemon juice for cream cheese mixture
- 2 large eggs room temperature
- 118.29 ml ½ cup vegetable oil
- 118.29 ml ½ cup Lifeway Organic Plain Whole Milk Kefir, room temperature
- 59.15 ml ¼ cup lemon juice (for muffin batter)
- 1 tsp vanilla extract
Instructions
- Prepare the Dry Ingredients: In a medium-sized mixing bowl, whisk together the flour, baking soda, baking powder, and salt. Make sure all ingredients are evenly distributed, and set the bowl aside. This will ensure your muffins rise evenly and the flavors are balanced. Measuring the flour by weight using a kitchen scale is highly recommended for precision and best results.
- Create the Lemon Sugar Mixture: In a separate bowl, combine the granulated sugar and lemon zest. Use your fingers to rub the zest into the sugar, pressing it together until the sugar becomes fragrant and slightly moist. This step is key to infusing the sugar with a deep lemony flavor. Set aside ¼ cup of this lemon sugar mixture for the cream cheese swirl, and reserve the remaining ¾ cup for the muffin batter. The sugar-zest blend will help enhance the muffin's flavor and provide a burst of citrusy freshness.
- Prepare the Cream Cheese Mixture: In a medium bowl, beat the softened cream cheese with the ¼ cup of lemon sugar and 1 tablespoon of lemon juice using a hand mixer or a whisk. Beat until the mixture is smooth and creamy, with no lumps remaining. The lemon sugar mixture will give this swirl a sweet, tangy note that pairs wonderfully with the muffins. Set this aside for later.
- Mix the Wet Ingredients: In a large mixing bowl, whisk together the eggs, vegetable oil, kefir, ¼ cup of lemon juice, and vanilla extract. Continue to whisk until everything is fully combined and smooth. The kefir in this recipe adds moisture and a mild tang, while the vanilla enhances the overall flavor profile. Be sure the ingredients are at room temperature, as this will help them blend more easily and create a smoother batter.
- Combine Wet and Dry Ingredients: Gently fold the dry ingredients from Step 1 into the wet mixture from Step 4. Use a spatula or spoon to carefully mix the ingredients, ensuring there are no streaks of flour left. Be careful not to overmix, as this can lead to dense muffins. Stir just until the flour is incorporated into the wet ingredients, and the batter has a uniform consistency. The batter will be thick but still pourable, which is just how it should be.
- Swirl in the Cream Cheese Mixture: Add about two-thirds of the cream cheese mixture (from Step 3) to the muffin batter and gently fold it in using your spatula. Don’t over-mix; you want to leave streaks of cream cheese throughout the batter, which will create a beautiful swirl in each muffin. This step is where the magic happens – the creamy swirl gives the muffins a luscious, tangy texture and flavor.
- Fill the Muffin Pan: Line a 12-cup muffin pan with paper liners or lightly grease each cup. Using a spoon or an ice cream scoop, evenly distribute the muffin batter into the muffin cups, filling each one about ¾ full. The batter should rise well and provide a generous, fluffy muffin once baked.
- Add the Final Cream Cheese Swirl: Take the remaining cream cheese mixture and drop about 1 teaspoon of it on top of each muffin. Use a toothpick or a skewer to gently swirl the cream cheese into the muffin batter, creating a marbled effect. Be careful not to mix it in too much – the swirl is meant to stay on top and bake into the muffin, forming a decadent, creamy topping.
- Bake the Muffins: Place the muffin pan in the oven on the middle rack. Bake at 425°F (220°C) for the first 5 minutes. This initial high temperature helps the muffins rise and form a golden, slightly crisp top. After 5 minutes, without opening the oven door, reduce the temperature to 350°F (175°C) and continue baking for 8 to 12 more minutes. The total baking time will range from 13 to 17 minutes. Keep a close eye on the muffins after the temperature is reduced, as oven temperatures can vary. You’ll know they’re done when a toothpick or cake tester comes out clean, and the muffins are golden brown.
- Cool the Muffins: Once the muffins have finished baking, remove them from the oven and let them cool in the pan for about 5 minutes. This brief resting period allows the muffins to firm up and makes them easier to remove from the pan. After 5 minutes, transfer the muffins to a wire cooling rack to cool completely. Allowing the muffins to cool fully will help preserve their fluffy texture and prevent them from becoming soggy.
- Serve and Enjoy: Once the muffins have cooled slightly, they’re ready to enjoy! These Lemon Cream Cheese Muffins are perfect for a quick breakfast or as an afternoon snack with a cup of tea or coffee. You can also store them for later use, making them an excellent option for meal prep.
Notes
- Ingredient Measurement: For best results, use a kitchen scale to weigh the flour. This ensures accuracy and helps achieve the right texture for the muffins.
- Room Temperature Ingredients: Make sure both the eggs and cream cheese are at room temperature. This will help them blend smoothly into the batter without lumps and promote a lighter, fluffier muffin.
- Lemon Zest: Fresh lemon zest is key to intensifying the lemon flavor. Avoid using bottled lemon juice as it won’t give the same fresh, zesty taste.
- Cream Cheese Consistency: Ensure the cream cheese is soft enough to mix easily but not too runny. It should be spreadable for the swirl but firm enough to hold its shape in the batter.
- Baking Tip: For even baking, do not open the oven door when reducing the temperature from 425°F to 350°F. This helps maintain consistent heat and prevents the muffins from sinking.
Chef’s Secrets: Achieving Perfect Muffins Every Time
To ensure these Lemon Cream Cheese Muffins come out light, fluffy, and flavorful, there are a few key tips to follow.
First, be gentle when folding the dry ingredients into the wet mixture—overmixing can result in dense muffins.
Aim for a few folds until the flour is just incorporated.
Secondly, don’t skip the step of rubbing lemon zest into the sugar.
This releases the oils from the zest, intensifying the lemon flavor throughout the muffins.
Lastly, the two-step baking process (starting at a high temperature and then lowering it) is essential for creating a nice rise and golden color without over-baking.
Serving Suggestions: Enjoy with Your Favorite Pairings
These muffins are versatile and pair well with a variety of beverages and snacks.
For a light breakfast or brunch, serve them alongside a fresh fruit salad, a cup of herbal tea, or a latte.
The creaminess of the muffins and the tanginess of the lemon make them a delightful accompaniment to a rich cup of coffee or a frothy cappuccino.
If you’re looking for something savory, try serving them with a side of yogurt or scrambled eggs.
They also make a fantastic snack on their own or can be served as a light dessert with a drizzle of honey or a dollop of whipped cream.
Storage Tips: Keep Your Muffins Fresh Longer
To keep your Lemon Cream Cheese Muffins fresh, store them in an airtight container at room temperature for up to 5 days.
If you live in a particularly warm or humid area, consider refrigerating them for longer shelf life.
For even longer storage, you can freeze these muffins for up to 1 month.
To freeze, place them in a freezer-safe bag or container, separating layers with parchment paper.
When you’re ready to enjoy them again, simply reheat them in the oven at 300°F for about 5–7 minutes to restore their fresh texture.
Frequently Asked Questions:
1. Can I substitute kefir with buttermilk?
Yes! If you can’t find kefir, buttermilk is a great substitute.
It will give the muffins a similar tang and moisture, resulting in a comparable texture and flavor. You can use the same amount of buttermilk (½ cup) in place of kefir.
2. Can I use a different oil for this recipe?
Absolutely! While vegetable oil is recommended for its neutral flavor, you can use other oils like canola oil, melted coconut oil, or even olive oil if you prefer.
Keep in mind that oils with stronger flavors, like olive oil, may slightly alter the taste of the muffins.
3. How can I make these muffins gluten-free?
To make these muffins gluten-free, you can substitute the all-purpose flour with a 1:1 gluten-free flour blend.
Make sure to check the blend contains xanthan gum or another binding agent to help the muffins rise properly.
4. Can I add other fruits to the muffins?
Yes, feel free to experiment with different fruits! Blueberries, raspberries, or even strawberries would pair beautifully with the lemon flavor.
Just be sure to gently fold them in to avoid breaking the fruit and making the batter too wet.
5. Why did my muffins sink after baking?
If your muffins sink after baking, it could be because of overmixing the batter or opening the oven door too soon during the baking process.
Be sure to only mix until the flour is incorporated and avoid opening the oven until the temperature has been reduced. This will help ensure the muffins maintain their rise.