Pumpkin Swirl Cheesecake Yogurt Cupcakes

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These pumpkin swirl cheesecake cups are made light with Greek yogurt and swirled with pumpkin butter on top.

These cheesecake cups are made light with Greek yogurt and swirled with pumpkin butter on top. Vanilla wafers on the bottom of these cheesecake cups create a simple, no-fuss crust. When the cheesecake cups bake, the cookies soften and all the flavors work together.Pumpkin Swirl Cheesecake Yogurt Cupcakes

Vanilla wafers on the bottom of these cheesecake cups create a simple, no-fuss crust. When the cheesecake cups bake, the cookies soften and all the flavors work together.

A few more healthy pumpkin desserts I love are Mini Pumpkin Chocolate Chip Muffins, Pumpkin Spice Snickerdoodles and Pumpkin Pie.

Fall is one of my favorite times of the year fro its’ sweater weather and pumpkin spiced lattes and desserts. I usually make this pumpkin butter recipe every Fall, but you can also buy it at Trader Joe’s.

More Pumpkin Desserts you might enjoy:

These cheesecake cups are made light with Greek yogurt and swirled with pumpkin butter on top. Vanilla wafers on the bottom of these cheesecake cups create a simple, no-fuss crust. When the cheesecake cups bake, the cookies soften and all the flavors work together.
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5 from 3 votes
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Pumpkin Swirl Cheesecake Yogurt Cupcakes

117 Cals 4 Protein 16 Carbs 5 Fats
Prep Time: 25 mins
Cook Time: 25 mins
Total Time: 50 mins
Yield: 12 Servings
COURSE: Dessert
CUISINE: American
These pumpkin swirl cheesecake cups are made light with Greek yogurt and swirled with pumpkin butter on top.


  • 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
  • 1 tbsp all purpose flour
  • 3/4 cup pumpkin butter or pumpkin pie filling


  • Heat oven to 350°.
  • 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. Gradually beat in fat-free yogurt, egg whites and flour. Do not over beat. Pour into cupcake liners filling half way.
  • Top each with 1 tbsp of the pumpkin butter. Using a toothpick, swirl the pumpkin butter into the cream cheese mixture for a marbling effect.
  • Bake 25 minutes or until center is almost set. Cool to room temperature. Chill a few hours in the refrigerator before serving.


Serving: 1cup, Calories: 117kcal, Carbohydrates: 16g, Protein: 4g, Fat: 5g, Cholesterol: 2mg, Sodium: 24mg, Fiber: 0.5g, Sugar: 12.5g
WW Points Plus: 3
Keywords: pumpkin cheesecake cupcakes, pumpkin desserts, pumpkin swirl, Pumpkin Swirl Cheesecake, swirls cheesecake

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  1. Could these be baked in ramekins rather than in a cupcake tin with liners?

  2. Soo good! Favorite fall dessert

  3. Is it the mini cupcake holders or the regular ones?

  4. Will almond flour and xylitol work instead of flour and sugar? I’m diabetic and have to cut carbs, but I have been craving something pumpkin.

  5. These are fantastic. Second time making them in a week ? I used mini oatmeal cookies from Sprouts broken up for the crust. Absolutely recommend! 

  6. I absolutely love this recipe! The cheesecake itself is decadent! I’m not in love with the vanilla wafer crust so I would make it with a different crust next time, but other than that it’s a delicious, healthy fall treat 🙂

  7. Can these be made in mini pie crusts? Would the cooking time change? 

  8. Can you freeze these?

  9. Can the all purpose flour be left out? Or can wheat flour be used instead? 

  10. Love all your recipes. This one is in the oven. Could not find wafers here so my base is Grape Nuts, ground almond, ground flax and enough brown butter to bind. Made the pumpkin butter days ago and we just can’t get enough of it.  Thank you !!!

  11. Pingback: Pumpkin Spice English Muffin Cheese "Danish" • Simple Nourished Living

  12. Just made these for Thanksgiving and couldn’t be happier. They are great. I used gingersnap cookie for the bottom. Used part non fat free cream cheese and part reduced fat. Used “Swerve” sugar replacement, and an unsweetened pumpkin butter. Love these. Will have to make them often as I am a big pumpkin fan. All of your cheese cake recipes work so well. Thank you!

  13. Can I make these the day before serving?  Or do I need to make them the same day?

  14. If I substitute Splenda will it change the carb content? my dad is diabetic and needs to watch his carbs 

  15. Hi, would Maple Pumpkin Butter work or will that alter the intended flavor too much? I live near Sprouts and I don’t think they carry plain Pumpkin Butter. Thanks for the advice! Looking forward to trying these!

  16. Can I use coconut sugar instead!?  Or would the amount change? These look amazing! 

  17. Have you made these with truvia? These look good but I’d want to cut the points a little

  18. Gina, I have a lot of left over fat-free vanilla yogurt. Can I use that instead of the greek yogurt?

  19. Can you use almond or coconut flour instead?

  20. I’m thinking gingersnaps instead of Nella wafers.

  21. How many smart points?

  22. Could you make these into mini-cupcakes instead? How would that change the baking time?

    • It will change.  I don’t know by how much but will be less.  I believe the recipe says 25 mins.  I would check them at 15 and Keep checking it every 3 -5 minutes until done per the directions

  23. I made these using ginger snaps instead of nilla wafers. They came out excellent!

  24. Can I swirl in another flavor? Making for family gathering and already have pumpkin pie so want another flavor?

  25. Can you use the new Challenge Neufchatel Cheese for this recipe? I have never really understood the difference between Neufchatel and cream cheese anyway. The new Challenge Neufchatel is 1/3 less fat.

  26. Im making these tomorrow for my intern buddies, but instead of using vanilla wafers I'm using the skinny pumpkin spice sknickerdoodle cookies! So excited!

  27. WOW, everyone Loves this recipe!So far I have made Pumkin (pureed pumkin and pumkin spice) topped with 2 marshmallows, Apple pie (apple pie filling) topped with Pecans, Country Lemon (Lemon pie filling) toped with 3 pecans, Rasberry Chocolate (Semi Sweet) Today it will be Smores. One thing I have noticed was that using the larger Muffin pan and jumbo cups keeps the ingredints contained.
    Place the cookie in and 1/2 of a table SPOON mix, enough to cover the bottom, then put the (FLAVOR MIX)in and top with cream cheese mix, this ensures an easy distrubution of mix. Also I noticed that room temp topping combined better. I am also going to try a TOFU Lactose Free and see how that work with that are lactose intolerant. I also substituted Truvia for the Sugar and the difference was unnoticed (infact used slightly less then the recommeded amount).

  28. Yummy! I made the pumpkin butter which was soooo good! Then made the little cheese cake swirls that have been quickly disappearing from the fridge…by me! I'm the pumpkin lover in the house and have been in heaven with your pumpkin madness recipes! Thanks so much for sharing your recipes, photography and love of cooking!

  29. Made these tonight! I used the pumpkin butter recipe, whole wheat flour instead of white, and crushed graham cracker instead of vanilla wafers. Turned out AMAZING. =)

  30. Can't wait to try these, thinking of using the pumpkin dip as icing 🙂

  31. I used graham cracker instead of nilla. And Domino stevia/sugar blend instead of sugar. They are so good. Thanks!

  32. Whipped these up earlier and they are in the frig!! 🙂 I may have to sneak one for breakfast tomorrow morning!

  33. Do you have to use the greek yogurt … im not a huge fan of any greek yogurt so can i just skip that part and do everything else or will it make a huge difference

  34. I made these this weekend for a family get together… They were gone in less than 3 minutes 🙂 Thank you Gina for wonderful recipes.

  35. I've never seen a website where people who have not made the recipe comment on how good it looks. Save your review for AFTER you've made it so you can comment with something that is helpful.

  36. Made last night and very yummy. Recipe is a keeper!

  37. Could I use Splenda instead of sugar?

  38. Made tonight with strawberry Jam on top. They were awesome! How do I keep them from falling in the center?

  39. Making them for my mother's birthday tonight…the kitchen smells wonderful with the pumpkin butter on the stove!

  40. I made these the other day when I had my parents over for dinner…every one loved them. I have been watching a lot of food network lately and decorated them up a bit (not sure how many points that added). I posted a pick on my blog http://myyo-yojourney.blogspot.com/

  41. These are DELICIOUS! I made them last night to serve today (Thanksgiving) but had to taste the finished product. This is a very easy recipe and I know they will be gone as soon as I put them out.

  42. I dont have any sugar, can I use brown sugar or agave nectar??

  43. They needed just a pinch of salt on top and came out good!

  44. Not too sure?

  45. Thank you, these are delicious!
    Can they be frozen?

  46. These are regular sized.

  47. What size of cupcake do these make? the mini or regular size?

  48. Finally got a chance to make these (with your pumpkin butter, too). So delicious. Husband approved too.

  49. SOOOOOO Good!!! Gina, I think I love you! 😀
    I made this with strawberry preserves instead of the pumpkin butter and they came out perfect. thanks so much

  50. I had a girls lunch today and my friend made these pumpkin swirl cheesecake cupcakes. Loved them! They were not overly sweet but so creamy. I am turning everyone on to Skinny Taste. This is now my first "go to" place for recipes.

  51. I just made these. They are quite yummy however, I couldn't find pumpkin butter only apple butter. So I used pumpkin pie filling and added some cinnamon and vanilla. Next time Ill add some sugar to it. The pumpkin was bland to me. The cheesecake part is deelish!

  52. I made these tonight and they were absolutely delicious! I don't know how I would stay on plan without you, thank you for all your hard work and dedication!

  53. I made these and your chocolate oatmeal cookies this week and they are both absolutely delicious! Thank you so much for your wonderful recipes!

  54. Thank you, thank you, a MILLION times thank you for this blog. I found you the week I joined WW and would totally have given up if not, because I adore food and food blogs and couldn't live without the joy they bring on a growling, jealous stomach – now I don't have to!

    This recipe was amazing, I used your homemade pumpkin butter and added cardamom and nutmeg because I'm a savory kind of girl – nom, nom.

    I've already made three of your recipes in a week and I'm sticking with them until I get the skinny cooking gist on my own! Seriously I cannot thank you enough!!!

  55. Your recipes are all awesome. I have made 4 or 5 since stumbling on this website last weekend. I'm printing out the recipes as I try them! Thanks!!!

  56. Yum!! I made these today and I was a little unsure about them before I started. I really LOVE cheesecake and most of the time substitutes for the real thing just dont do it for me….these were fantastic!! The homemade pumpkin butter made it even better. Thank you! We will be having these again!!

  57. Hey, do you think almond butter would work here as well? looks so deliciouss!

  58. I made a "gluten free" version to accommodate the doctor I work with. Instead of the vanilla wafer I make a crumble out of GF flour, brown sugar, pecans, cinnamon, nutmeg, salt and butter and pressed it into the bottom of the liners. I also added GF flour to the cheesecake portion as well. I must not have read the recipe correctly because I also bought plain pumpkin puree as well. I just added some cinnamon, nutmeg and sugar to flavor it.

    This is DEFINITELY a recipe that will appear in my kitchen over and over again!

  59. You're going to have to add sugar, vanilla, and pumkin pie spice to it or it will be pretty bland.

  60. I tried these today but instead of pumpkin pie filling i picked up pumpkin puree by accident hopefully it taste the same LOL

  61. Wow! Excellent cupcake recipe! Thank you for sharing it with us!

  62. These are AMAZING! Just made them today. They totally hit the spot. I felt like I was eating a real dessert!

  63. Oh my goodness – these look delightful! Thanks for the recipe!

  64. I loved these and so did my husband! They were so easy to make, too! Thanks for this recipe. 🙂

  65. I made these yesterday and they were like little cheesecakes from Heaven! My local store was out of pumpkin pie filling so after thorough searching around the store I was able to find pumpkin butter. A tad pricey but it was a pretty big jar. That in itself tastes great. I brought them over to a friend's for dinner and her husband ate 3 of them! Very tasty!

  66. These look so yummy, I just love your recipes using pumpkin butter. Thank you!

  67. I am also so excited about fall and pumpkin season. I can't wait to see the rest of your pumpkin recipes! Do you have any that aren't sweet? (i.e. a main course that utilizes pumpkin?) Anything in the crock pot would be a bonus :-).

  68. At my house we try to avoid partially hydrogenated oils – vanilla wafers haven't caught up with the times yet!! For this recipe I used the 100 calorie pack lorna doons – I used three little cookies per cup and sort of crumbled them with my fingers. it adds .7 calories and .22 fat so I don;t think it changes the points value!!

  69. Thank you so much for all your wonderful recipes! I also sincerely appreciate the WW points values. I made these yesterday and brought them to a party. They were a big hit! Personally i thought they could have used a little more sweetener, so if i make them again, i'll probably double the sugar (actually i used the splenda baking blend which usually makes it even sweeter, so i thought that was odd.) Also I used pumpkin pie filling, not pumpkin butter… so perhaps pumpkin butter is sweeter?

  70. I made these this morning for a get-together of friends… did not tell anyone except for one other friend that is also dieting that they were "healthy"… they disappeared almost immediately! I crushed the nilla wafers instead of putting them in whole, and added about 1/4 tsp of pumpkin pie spice to the cheesecake mixture… SO GOOD!

  71. Thank you so much for posting this fabulous recipe! I just made these and the are perfectly yummy (and gorgeous). I can't believe I get to have my cheesecake and am still able to stick with my nutrition plan! Awesome!

  72. These are like little bites of cheesecake heaven! The only reason they are called cupcakes is the presentation.
    I did a batch with strawberry jam and gluten free gingersnap cookies. The jam boiled when it cooked, however and so they puffed all up like muffins, but when I took them out, they collapsed! They are very "artistic" looking, but delicious!
    I can't find pumpkin stuff yet… 🙁

  73. Loved these although I used leftover icing from the pumpkin cupcakes as the pumpkin flavor and then for a few of them used strawberry jam…both were excellent and my co-workers liked them as well. Did not feel like a lowcal treat at all!

  74. SOOOOO excited to see all of your pumpkin recipes!! I LOVE pumpkin and I LOVE fall!! Yay! Thanks Gina!!!

  75. Made them tonight, used FF cream cheese which gets each cupcake down to 2 WW points plus. I thought they were tasty, a good sweet treat, but they definately don't seem like "cupcakes" , more like Custard cakes. The texture just wasn't "cake-like" They are good frozen as well.

  76. And about freezing them, I don't see why you couldn't!

  77. I would say my homemade pumpkin butter Is better but if you don't have it, pumpkin pie filling is fine.

    Jordon, you made me laugh! Yeah I could see how that would be bland.

    You can make this gluten-free by either eliminating the cookie, or using a gluten free cookie instead.

  78. These look fabulous! Keep the pumpkin coming. I love it this time of year!

  79. Is the recipe better with the pumpkin butter or the pumpkin pie filling?

  80. Can I freeze these?

  81. I made these yesterday and they were delciious, about half gone already between three people!

    Unfortunately, I accidentally bought canned pumpkin instead of canned pumpkin pie mix, so it was totally lacking all those fall spices! overall, the cheesecake component was delicious and the pumpkin swirl just made it look pretty. Next time I will make sure to buy the right type of pumpkin! (pumpkin butter is really hard to find in the bronx haha!)

    – Jordan

  82. Oh my goodness gracious Gina, you've done it again. I have been eating up your no-bake pumpkin spice cheesecake but lack the self control to have just one slice. I've been hoping you'd come up with a pumpkin cheesecake cupcake recipe. (Yay built-in portion control!) I made your lemon ones a lot over the summer, plus a bunch of variations of it. So very excited to be making these tonight or tomorrow! Thank you x1000. 🙂

  83. Rich pumpkin heaven!

  84. Hello, I was wondering if this or any of the recipes can be made gluten free. If they can could you post some gluten free recipes on the site as well? Thank you

  85. I made these tonight, they were a hit! I had a problem with them sticking to the inside of the cupcake liners, and I plan to spray a little non-stick spray in them next time. I loved the way the pumpkin butter made my house smell while it was simmering, smells better than any fall themed air freshener out there!

  86. Wow – these look fantastic!!!
    I can't wait to make them for my biggest loser weight loss group!

  87. Dana, these should be refrigerated, I would say 3 days?

    Pamela- Try making them without the flour, it should still work. The flour helps bind it a little.

    Gram crackers would work, I would crush them first.

    Allison- Thank you, so glad everyone liked them!!

    Lola- absolutely!

  88. I love pumpkin! Keep these recipes coming…I've tried some of others on your site and they have all been good.

  89. Gina- these look delicious. Trader Joe's sells pumpkin butter that is fat free. do you think that's an acceptable substitute for your homemade version?

  90. Gina! I made your pumpkin cupcakes this weekend. I am pretty sure I ate 5 of them and then brought them to work to be shared. EVERYONE talked about how good they were. You have such a gift! Thank you for sharing, and I look forward to making these soon!

  91. Can I use reduced fat graham crackers as a crust instead of vanilla wafers? How would that work consistency wise?

  92. I think I'd still have trouble with portion control since it makes 12 🙂 Looks amazing!


  94. I'd like to make these gluten free. I can use a gluten free vanilla wafer. What about the 1 tbsp of flour? Could I substitute corn starch or use a gluten free flour instead? What is the purpose of the flour? Thx! 🙂

  95. Wow, these look incredible! Thanks so much for sharing. Love new Fall ideas. Come stop by my blog today for my very first giveaway. It's a yummy one, you won't wanna miss. 🙂

  96. i cannot wait to try this out! my husband and I love anything and everything pumpkin flavored.

  97. How long do you think these will keep? I'd love to "bake 'n take" some to our family Thanksgiving dinner . . .

  98. This website is my new BEST friend! I have loved every single (easy!) recipe that I have tried…not to mention the fabulous photos and enticing layout!

  99. This looks absolutely fantastic – can't wait to make them! But it seems the print button is out of whack – any chance we can get it fixed?? Thanks Gina for all these wonderful recipes – my husband and I have lost over 10 lbs each thanks to you! 🙂

  100. These sound so yummy! I have a recipe for cheesecake cupcakes that is so not good for you. I was wanting them but I wouldn't make them. Now I can have some!! Thanks for the recipe!!!

  101. If you don't like pumpkin, swirl in your favorite fruit preserves. Or for a fall theme, why not apple butter!

  102. love love LOVE all this pumpkin! keep it coming!

  103. I don't love pumpki, but I love the idea…any suggestions for a pumpkin substitution?

  104. I love pumpkin and looking forward to learn more recipes.

  105. Those look fantastic! Bring on the punkin recipes. I'm pinning this one. Thanks!

  106. These look DELISH!!!!

  107. These look delicious and so easy, love it!

  108. those as simply BEAUTIFUL.

  109. LOVE pumpkin anything…. bring it on!
    This recipe looks wonderful! I can't wait to try it soon.

  110. I'm fanatic for pumpkin, just love it love it!! And this cupcakes sound just perfect!

  111. I can't wait to see all the pumpkin recipes! I LOVE pumpkin! These look delicious!

  112. Oh my, I'm most definitely ready for pumpkin season to be here. These look delicious.

  113. Well, now I know what i'm making for dessert tomorrow! I can't get enough pumpkin! These look SOOOOOOO good!!!!!

  114. wow! these look amazing! yum 🙂

  115. Yum yum! Can't wait to make these!

  116. LOVE pumpkin! Yesterday I saw it in the store again after months of doing without. I now have an even dozen cans of yummy pumpkin. Bring on the recipes!

  117. These look amazing!! I am making these FOR SURE!

  118. I bet this would be amazing with gingersnap cookies on the bottom in place of the vanilla wafers! Not sure how it would affect the points, but I don't think those thin ginger cookies are very high in pts.

  119. These look so good! I loved the lemon yogurt cheesecake ones from before, and started to swirl in a bunch of ginger. Now I can't wait to add the pumpkin!

  120. I am definitely game for more pumpkin recipes 🙂 This is one of my favorite parts of fall! Delicious cheesecakes…I love the mini version.

  121. Wow! These look delicious. Fortunately, I can find canned pumpkin in Japan. Hooray! 🙂

  122. You are killing me with all these pumpkin recipes! But I LOVE it!!!! 🙂

  123. These look fantastic! Thank you so much for all the wonderful pumpkin recipes!


  124. Those look great! Thanks, Gina.

  125. these look great, can't wait to make these

  126. OMG! Have I died and gone to pumpkin heaven? Keep 'em coming, I cant get enough of the orange stuff this time of year.