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Lemon Cheesecake Yogurt Cups

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These lemon cheesecake cups are made with cream cheese, Greek yogurt and fresh berries. The “crust” is vanilla wafer cookies, so easy to make!

Lemon Cheesecake Cups
Lemon Cheesecake Yogurt Cups

Something about lemon says summer to me – perhaps, it’s the color? I’m not quite sure, but I do know the color yellow makes me happy and so do these little portion-controlled Lemon Cheesecake Yogurt Cups. More of my favorite cheesecake recipes you might love, these Maple Pecan Cheesecake ShootersRed, White, and Blueberry Cheesecake Cups and this Strawberry Cheesecake Dip.

Lemon Cheesecake Yogurt Cups

My mom always put vanilla wafers on the bottom of her cheesecake cups, which is such a simple solution to create a crust. Just put one wafer in the bottom of each regular-size muffin cup and top with the batter. The cookies will soften when the cheesecake cups bake. These individual lemon cheesecake cups make a great dessert. If you’re serving them for a party, you can make them the night before and refrigerate until it’s time to eat them.

While testing this lemon cheesecake recipe, I tried it two ways: the first, as seen in the photo, with blackberries on top, and the second with the berries mixed in with the cheesecake cups before I baked them. Both were equally good, but the berries on top are prettier.

What are lemon cheesecake cups made of?

  • Lemon: Lemon juice and zest
  • Creamy Ingredients: Softened 1/3-less fat cream cheese, fat-free vanilla Greek yogurt
  • Other Filling Ingredients: Sugar, vanilla extract, egg whites, all-purpose flour
  • Crust: Vanilla wafers


  • Sugar Substitute: If you’re trying to reduce your sugar intake, use monk fruit sweetener in place of sugar.
  • Lime Flavor: Make key lime cheesecake by swapping the lemons for key limes.
  • Crust: Switch out the Nilla Wafer with a gingersnap or chocolate wafer.
  • Lemon Cheesecake Toppings: Use whatever berries you want or a combo of mixed berries. You could even top it with pie filling or blueberry compote.

how to make Lemon Cheesecake CupsLemon Cheesecake Cups

More Cheesecake Recipes You’ll Love:

Lemon Cheesecake Yogurt Cups

5 from 6 votes
These lemon cheesecake cups are made with cream cheese, Greek yogurt and fresh berries. The "crust" is vanilla wafer cookies, so easy to make!
Course: Dessert, Snack
Cuisine: American
Lemon Cheesecake Cups
Prep: 10 mins
Cook: 25 mins
Cooling time: 30 mins
Total: 35 mins
Yield: 12 servings
Serving Size: 1 cupcake


  • 12 reduced fat vanilla wafers
  • 8 oz 1/3 less fat cream cheese, softened
  • 1/4 cup sugar
  • 1 tsp vanilla
  • 6 oz fat-free vanilla Greek yogurt, I used Chobani
  • 2 large egg whites
  • 3 tbsp lemon juice
  • 1 tbsp lemon zest
  • 1 tbsp all purpose flour
  • 24 blackberries


  • Preheat the oven to 350F.
  • Line cupcake tin with liners. Place a vanilla wafer at the bottom of each liner.
  • Gently beat cream cheese, sugar and vanilla until smooth using an electric mixer.
    beat bream cheese
  • Gradually beat in fat free yogurt, egg whites, lemon juice, lemon zest and flour. Do not over beat.
  • Pour into cupcake liners filling half way.
  • Bake 25 minutes or until center is almost set.
  • Cool to room temperature. Chill a few hours in the refrigerator.
  • Top with fresh berries and powdered sugar if desired.

Last Step:

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Serving: 1 cupcake, Calories: 108 kcal, Carbohydrates: 12 g, Protein: 3.5 g, Fat: 4.5 g, Saturated Fat: 3 g, Cholesterol: 6.5 mg, Sodium: 108 mg, Fiber: 1 g, Sugar: 9 g


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181 comments on “Lemon Cheesecake Yogurt Cups”

  1. Made half the recipe but used plain yogurt, it’s what I had on hand, so added 1 tbl additional sugar to make up the sweetness of a flavored yogurt.

  2. Every single thing I’ve made from skinnytaste is Devine- never ever fails! So grateful I can cook because of you!!!!! These little cheesecakes are insanely good!!!!!!!! Huge hit

  3. Avatar photo
    Deborah Woodbury

    I wonder if these would be good with a Trader Joe’s triple ginger snap cookie instead of the vanilla wafer????

  4. I made these for Father’s Day dinner. My dad can’t eat dairy other than cheese so I made them with almond and cashew yogurt. They were a big hit with even the pickiest eaters. I was not a fan. I would make them again with regular yogurt and definitely more lemon juice and zest. I used strawberries and blueberries instead of blackberries. 

  5. What do you think of switching lemon for lime as kinfod a key lime thing? What would you recommend for a garnish on top?

    1. I haven’t tried but I think it would be fine! Maybe top with raspberries? Check this recipe too

  6. Hi, Gina. Will you double check the points for this recipe? I just put all the ingredients into the WW recipe builder and it gave me 5 FS points for each. But, even it’s 5 points, this is a great dessert. I’ve made it before and it was a HUGE hit.

    Below is what I had entered.

    12item(s)reduced fat vanilla wafer(s) 13 Points
    8ozPhiladelphia Cream Cheese, 1/3 Less Fat 24 Points
    1⁄4cup(s)sugar 12 Points
    1tspvanilla extract 0 Points
    6ozfat free vanilla Greek yogurt 5 Points
    2item(s)egg white(s) 0 Points
    3Tbspfresh lemon juice 0 Points
    1Tbsplemon zest 0 Points
    1Tbspwhite all-purpose flour 1 Points
    1cup(s)fresh blackberries 0 Points

  7. I was wondering if Skyr (a type of Greek yogurt) could be used instead of the regular yogurt or would it be to thick?

  8. Pingback: 9 Lively Lemon Recipes | MyFitnessPal

  9. Pingback: 9 Lively Lemon Recipes – Fine Health Tips Collect

  10. Gina,
    Have you tried this with pumpkin? I’m looking for a low carb/low sugar alternative to Pumpkin pie for Thanksgiving for diabetic family members.

  11. Avatar photo

    I just made these since I had a brick of cream cheese to spare. I broke up bits of graham crackers as the base and they turned out fabulous!

  12. Since February is "National Heart Month" and next week is V-Day, my company sponsored a healthy dessert contest today. I would like to let you know that these cheesecake cups won me first place in that contest! 🙂 I credited your website of course. Thank you for sharing such a wonderful, light dessert that everyone enjoyed!

  13. A great recipe! Thanks for mentioning that diabetics can use Splenda instead of sugar. But one other observation is that low fat and fat free has more sugar content. As a diabetic I just used the regular product if sugar free cannot be found.

  14. These were delicious! So perfect for a weeknight dessert. Easy to make, and easy to control on the portion. I made these just as directed, and they came out just perfect. Yum!