Strained Yogurt Cheesecakes

Bite-sized cheesecakes that leverage yogurt strained to make cream cheese. Relax and enjoy these healthy, low-fat cheesecakes over and over!

About the ingredients for mini Yogurt Cheesecakes

Yogurt – Use any yogurt of choice, whether full fat/nonfat regular, Greek, or skyr yogurt. Some yogurts are tangier, or have a thicker consistency, which can affect the density and taste of the cheesecakes. 

If using vanilla flavored yogurt, skip the addition of vanilla.

Standard cheesecake recipes often incorporate sour cream or heavy cream as core ingredients. In this recipe, we substitute these ingredients with yogurt (1/2 cup yogurt for 1/4 cup sour cream and 1/4 cup heavy cream). 

Strained cream cheese yogurt – The section below covers the process of straining yogurt to make cream cheese as a preliminary step. Straining essentially removes the yogurt's whey, that is its residual liquid. The end product is a thick, cream cheese substitute we can use for cheesecakes.

Cream cheese – Any cream cheese works, whether low-fat or full fat; this recipe uses low-fat cream cheese, as fat free cream cheese is non-existent due to its low demand.

Sugar – Use granulated sugar or a substitute of choice. Another option is a combination of ½ tsp monk fruit powder and 2 tbsp sugar/sugar substitute.

Crust – These can be graham crackers, animal crackers, digestive biscuits, sugar free cookies, Oreo cookies, etc. Or, swap the crackers out for oat flour, ground pita chips or tortilla chips, almond or other nut flour accompanied by some sugar and cinnamon.

Margarine – Use butter or oil as a substitute, but not yogurt or water for a crisper, crunchier crust. 

Although flour can smooth out wrinkles and cracks, it can also contribute to a denser cheesecake. This cheesecake omits flour, as it holds up well without flour; and minor bubbles are also minimal and not a concern.

How to make make cream cheese from yogurt

One key, pre-work ingredient is making the strained yogurt. Strained yogurt entails removing enough whey liquid so that it resembles thick cream cheese. Here are the easy steps:
  1. Scrape yogurt into a fine mesh strainer placed over a bowl. Take care not to press yogurt through the strainer. Wrap plastic wrap over and around the strainer where exposed to air.
  2. Stir the yogurt daily; and remove any collected whey liquid (strained liquid in the bowl). Keep the whey liquid for its nutritional benefits (calcium, B vitamins [1]).
  3. Refrigerate for at least 3 days or until yogurt has a cream cheese consistency.
  4. The end result should be yogurt with a thick, cream cheese texture. Store any excess yogurt cream cheese in the freezer or refrigerate per the expiry on the yogurt. I like to make a big batch for other uses, such as spreads, or future cheesecakes.

Serves: 12
Prep Time: 10 minutes – Cooking Time: 20 minutes – Total Time: 30 minutes

Helpful equipment

  • Fine mesh strainer to fit over a bowl
  • Cupcake/muffin liners
  • Muffin tin to hold cupcake/muffin liners
  • Electric mixer or stand mixer


For the crust:
  • 1 cup crushed crackers
  • 2 tbsp. melted margarine

For the filling:
  • ½ cup nonfat yogurt
  • ½ cup lowfat cream cheese (8 oz), room temperature
  • ½ cup strained nonfat yogurt cream cheese (read blog)
  • ½ tsp vanilla extract (skip if using vanilla yogurt)
  • ½ tsp lemon zest
  • ¾ cup granulated sugar (or ½ tsp monk fruit powder + 2 tbsp sugar of choice)
  • Pinch of salt
  • 6 tbsp. liquid egg whites or 2 eggs


Step 1
Preheat oven to 325 F.

Step 2
Place crackers in a food safe storage bag and pound until fine. Or, use a food processor to pulse crackers until fine.

Step 3
Melt margarine over low heat in a saucepan. Add crumbs to the saucepan (or margarine to the food processor) and thoroughly combine. Lay cupcake liners down in a muffin tin. Press crumbs into the bottom of each cupcake liner. Bake cupcake liners for about 10 minutes until the crust is crisp. Remove and allow to cool.

Step 4
In a mixing bowl with an electric mixer or stand mixer, beat together yogurt, cream cheese, sugar, vanilla extract if using, lemon zest and sugar until combined well. Take care not to introduce too much air. Mix in the eggs slowly by hand, being careful not to whip them.

Step 5
Pour batter into cupcake liners, distributing evenly and filling to either ½ or ¾ full. Bake until a thermometer inserted into the center registers 165 F and the tops have smoothed and puffed, about 15-22 minutes, depending on size. Remove and cool to room temperature. The cheesecakes will deflate after cooling. Refrigerate to firm up, about 2 hours.

Step 6
Garnish with desired toppings: fruit/fruit sauces, frostings, whipped cream, nuts, cookies, nut butters, melted dark/white chocolate, chocolate chips, toffee, butterscotch, caramel, fudge, pie filling, crackers, candy, pretzels, matcha, sugar, etc.

Step 7
Serve or store covered in the refrigerator.


  • The tops will crack if overbaked.
  • A toothpick inserted into the center will come out seemingly under-cooked and wet with batter, but that is ok. The cheesecakes will firm up in the refrigerator.
  • Adding 2 tsp flour to the batter will smooth out cracks and lines, but is unessential for these cheesecakes. They hold up well without flour.
  • 18-20 minutes in the oven work best for me.

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