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Healthy Pumpkin Cheesecake Bars is a low calorie and low fat cheesecake recipe made higher protein with Greek yogurt and a simple, gluten-free crust. Perfect for fall baking!

It’s no secret that I love all things pumpkin! Fall is my favorite time of year and I look forward to making all the healthier pumpkin recipes every fall.
Truthfully, I can eat low calorie pumpkin cookies and healthy pumpkin muffins all year round if I let myself.
And now I’ve got this pumpkin cheesecake recipe to add to the list! It’s a simple, yet delicious fall dessert. The best part is this low-fat cheesecake recipe is easy to make and it’s a higher protein cheesecake with the addition of Greek yogurt.
Table of Contents
- What Makes This Cheesecake Recipe Healthier?
- ***5 Star Review**
- Ingredients For Low Sugar Cheesecake
- How To Make Low Calorie Cheesecake
- Substitutions For Pumpkin Cheesecake
- How To Serve Cheesecake
- More Low Fat Fall Dessert Recipes
- More Low Fat Cheesecake Recipes
- Healthy Pumpkin Cheesecake with Greek Yogurt Recipe

What Makes This Cheesecake Recipe Healthier?
This healthy cheesecake recipe is a lower fat version of cheesecake and here’s how we do that.
Low In Fat – This lighter cheesecake recipe uses Greek cream cheese which is significantly lower in fat that lower fat cream cheeses. The recipe combines Greek yogurt with the Greek cream cheese, or Neufchatel which is a lower fat cream cheese with fewer calories. This how simple it is to make a low calorie pumpkin cheesecake!
Lower In Sugar – Most cheesecake recipes have 20 grams or more of added sugar. This has just 3 grams of sugar per bar using a zero calorie sweetener.
Higher Protein – This healthy cheesecake recipe uses Greek cream cheese and Greek yogurt which increases the protein content without sacrificing flavor. You always want higher protein in a recipe to maintain blood sugar and reduce cravings.
Higher Fiber – This recipe uses gluten-free flour which is higher in fiber than other cheesecake recipes that use white flours or graham crackers. High fiber is important for fullness, weight loss and weight management.
Lower Calories – Most cheesecake recipes range from 400-600 calories. This recipe is 188 calories per bar.
***5 Star Review**
I never write reviews but felt that I needed to on this one and it was my first experience baking gluten free. I followed the recipes exactly. These pumpkin bars turned out AMAZING! They are so easy to make, taste really good and most importantly, healthier than a regular pumpkin dessert. I love these! – Marci

Ingredients For Low Sugar Cheesecake
- Gluten Free Baking Flour
- Coconut Sugar
- Extra Virgin Olive Oil
- Unsweetened Almond Milk or milk of choice
- Greek yogurt, nonfat
- Greek cream cheese or Neufchatel
- Vanilla Extract
- Stevia
- Cinnamon, Ground Ginger, Nutmeg, Salt
See the recipe card below for exact ingredient amounts, nutritional information, and detailed instructions.

How To Make Low Calorie Cheesecake
The first step to making deliciously low calorie cheesecake bars is making the crust. Combine the ingredients for the crust in a bowl then transfer to a baking pan then bake.
Once the crust has fully cooled to room temperature after baking, prepare the filling by mixing together the ingredients for the filling. Then pour the filling over the crust and smooth into an even layer. It’s very important that the crust be cooled to room temperature before you do this step to ensure the crust does not crack.
Bake the cheesecake then remove from the oven and cool to room temperature before freezing to set and store in an airtight container. After it has set, slice and serve your healthy cheesecake!

Substitutions For Pumpkin Cheesecake
Here are a few substitutions for this pumpkin cheese cake with Greek yogurt. Please note that when you make substitutions to a recipe it will alter the nutrition, calories, fat, carbohydrates and protein content.
- Gluten Free Flour – You can substitute gluten free oat flour with this recipe. Coconut flour will not work with this recipe. I have not tested almond flour, but my guess is it will work. I would try 1 1/4 cups of almond flour. White and whole wheat flours I never recommend using and I never bake with them myself so I cannot speak to how they would work.
- Stevia/Sugar – You can substitute the coconut sugar in the crust for stevia and/or substitute the stevia in the cheesecake filling for coconut sugar. I do not recommend substituting honey or maple syrup as I suspect it will make the filling too runny and the crust will not stick together.
- Greek Yogurt – You can substitute a dairy free yogurt like plain almond or coconut yogurt. These yogurts may not be as thick as Greek yogurt so the consistency may not be equivalent to cheesecake.
- Greek Cream Cheese – You can substitute low fat cream cheese for the recipe. Dairy free cream cheese may also be substituted, but note that with dairy free options the consistency may be different than what you expect.
- Pumpkin Pie Spice – You can use this in place of the nutmeg, ginger and cinnamon. If using pumpkin pie spice, I recommend still adding a quarter teaspoon of cinnamon to the recipe.

How To Serve Cheesecake
To serve this crustless pumpkin cheesecake, I recommend removing the cheesecake bars from the freezer (they should be stored in an airtight container) and placing them in the refrigerator for two to three hours before enjoying.
Enjoy your healthy pumpkin cheese cake with a cup of healthy pumpkin spice latte or a pumpkin protein smoothie!
You can also make your healthy pumpkin cheesecake part of a meal with a warm bowl of chicken sausage chili or this comforting and healthy chicken pot pie casserole!
More Low Fat Fall Dessert Recipes
Yes, you can make cheesecake with cottage cheese! You can replace the Greek yogurt in this cheesecake recipe with blended cottage cheese. Blend the cottage cheese until very smooth in a food processor or blender.
Yes, cheesecake can be incorporated into a healthy diet. The context of what is healthy depends on what your overall diet, calories and nutrition looks like. One food doesn’t make you healthy or not healthy especially if you are enjoying it from time to time. Enjoying lower fat cheesecake options may be helpful in controlling overall calories you consume lower like this low-fat pumpkin cheesecake recipe.

















I never write reviews but felt that I needed to on this one and it was my first experience baking gluten free. I followed the recipes exactly. These pumpkin bars turned out AMAZING! They are so easy to make, taste really good and most importantly, healthier than a regular pumpkin dessert. I love these! Thank you Megan!
Will these stay together if you leave out the crust?
I haven’t tried it myself, but I suspect they would especially if you chill them in the freezer long enough.