Mini High Protein Keto Cottage Cheese Cheesecake

This mini high-protein cottage cheese cheesecake is a delicious low-carb dessert that fits perfectly into a keto diet. It’s a baked cheesecake made with cottage cheese (for extra protein) and a simple almond flour crust, so it stays low in carbs and gluten-free. Each little cheesecake packs about 10 grams of protein and only a few grams of net carbs per serving. If you love keto desserts like this, be sure to check out the Ultimate Keto Recipe Cookbook for hundreds of easy, low-carb recipes. In this post, we’ll cover all the ingredients, step-by-step instructions, tips for success, and even some tasty lemon and berry variations to try.

Ingredients & Benefits

Almond flour (1.5 cups) – Almond flour is a staple keto baking ingredient. It’s low in carbs and rich in healthy fats and protein. One ounce (about 28 g) of almond flour provides roughly 6 g protein and 14 g fat, but only about 5 g total carbs (with 3 g fiber). That makes it perfect for a keto crust that won’t spike your blood sugar. Almond flour also contributes vitamin E, magnesium and other nutrients.
Butter (4 tablespoons, melted) – Adds rich flavor and helps bind the crust. In keto baking, healthy fats like butter are encouraged to keep carbs low.
Granular low-carb sweetener (2 tablespoons) – Use a sugar-free sweetener such as erythritol, monk fruit, or a blend (like xylitol + stevia). These sweeteners provide sweetness with virtually zero net carbs, so they won’t affect ketosis. Adjust the amount to taste.
Salt (pinch) – Enhances overall flavor. Just a pinch of salt in the crust and batter brings out the cheesecake’s richness.
Cottage cheese (1 cup) – The star ingredient for high protein. Cottage cheese has about 12–15 grams of protein per ½ cup serving, while remaining relatively low in carbs. (For example, a ½ cup of cottage cheese typically has only ~4–5 g carbs but ~12–15 g protein.) In this cheesecake, cottage cheese makes the filling extra creamy and boosts protein content. It’s even higher in protein than cream cheese by volume, helping to maintain muscle and keep you feeling full. Cottage cheese also contains calcium and probiotics (if live cultures) for added health benefits.
Full-fat cream cheese (2 ounces) – Adds the classic cheesecake creaminess and fat. Cream cheese is mostly fat, with minimal carbs (about 1 g per ounce) and 1–2 g protein per ounce. It contributes to the rich texture and traditional flavor of cheesecake.
Sour cream (2 ounces) – Keeps the filling tangy and smooth. Full-fat sour cream is very low in carbs (about 1 g per ounce) and mostly fat, making it keto-friendly. It also contains a little protein. The fat in sour cream helps make the cheesecake silky and satisfying.
Eggs (2 large, room temperature) – Eggs bind the filling and add structure. They’re also nutritious: each large egg provides about 6 g protein and important vitamins (A, B12, selenium and others). Including eggs makes the cheesecake higher in protein and rich in nutrients, helping the dessert set up firmly when baked.
Vanilla extract (1 teaspoon) – For flavor. A small amount of pure vanilla extract adds depth and sweetness without carbs. (You can also use liquid stevia or a tiny bit of flavored protein powder instead if you like.)
Salt (pinch) – A pinch in the filling balances sweetness and enhances the overall taste.
Optional – Lemon zest & juice (1 teaspoon each) – For a lemon cheesecake variation, add 1 teaspoon grated lemon zest and 1 teaspoon fresh lemon juice to the filling. This brightens the flavor without adding significant carbs.
Optional toppings – Fresh berries (strawberries, raspberries, blueberries) or a sugar-free whipped cream are great low-carb toppings. Berries add natural flavor and antioxidants while keeping carbs moderate.

Each of these ingredients plays a role: the nutty almond crust keeps the carbs low while giving fiber and healthy fats, and the dairy (cottage cheese, cream cheese, sour cream) provides most of the protein and fat for a creamy, filling cheesecake. Together, they make a dessert that satisfies sweet cravings without knocking you out of ketosis.

Instructions

Follow these steps to make four mini cheesecakes (or one small cheesecake) with almond crust. The directions are beginner-friendly and include tips as we go:

Preheat & prepare crust. Preheat your oven to 350°F (175°C). Grease four 6-ounce ramekins or a 6-inch springform pan (8×2 inch), or line them with parchment paper. In a medium bowl, combine 1.5 cups almond flour, 4 tablespoons melted butter, and 2 tablespoons low-carb sweetener (and a pinch of salt). Stir until the mixture is well combined and crumbly. You should be able to press it together. Distribute this crust mixture evenly among the ramekins (or press it into the bottom of the springform pan), about 2–3 tablespoons per ramekin. Use the back of a spoon or your fingers to firmly press the crust into a flat, even layer at the bottom. For best results, you can pre-bake the crust for 5–8 minutes just until slightly golden (this helps it firm up), but it’s optional. Tip: Line your baking sheet with parchment paper for easy cleanup.
Drain the cottage cheese (optional). To ensure a ultra-smooth filling, you can place the cottage cheese in a fine mesh sieve or cheesecloth over a bowl and let it drain for 10–15 minutes. Press gently to remove excess whey. Draining gives a thicker texture and prevents the cheesecake from being watery. (If you’re in a hurry, you can skip this step – the food processor will blend lumps.)
Mix the filling. In a blender or food processor, combine 1 cup drained cottage cheese, 2 ounces cream cheese (cubed for easy blending), 2 ounces sour cream, 2 large eggs, 1 teaspoon vanilla extract, and a pinch of salt. Add sweetener to taste (start with 2 tablespoons of powdered erythritol or monk fruit; adjust based on your preference). Blend or process until the mixture is completely smooth and creamy. Scrape down the sides as needed. At this stage you can also stir in any lemon zest/juice if making the lemon variation. Tip: For an even lighter texture, blend until the mixture is totally lump-free. You may need to stop and scrape a couple times. Using a high-speed blender or food processor works best to fully break down the cottage cheese curds.
Assemble & bake. If you pre-baked the crust, place the crust-lined pan back into the oven just to warm slightly. Pour the cheesecake filling evenly over the crust in each ramekin (or into the 6-inch pan). The filling will be loose. To help it bake evenly, set the ramekins (or springform) on a baking sheet. For extra insurance against cracks, use a water bath: Carefully pour hot (not boiling) water into the baking sheet so it comes about ½–1 inch up the sides of the ramekins/pan. This moist heat keeps the cheesecake from drying out or cracking. If you prefer not to use a water bath, skip it, but be aware the center may set slightly differently.
Bake. Place in the oven and bake for about 25–30 minutes at 350°F, until the edges of the cheesecake are set and the center is still slightly jiggly. (If you’re using a larger pan or thicker cheesecakes, you could bake at 350°F for 30–40 minutes, or as in some recipes 375°F for 40–45 min. But for mini ramekins, 25–30 min should suffice.) Tip: The cheesecake will continue to cook from residual heat, so avoid overbaking. It’s done when the top looks set and the center quivers just a bit.
Cool gradually. Once baked, turn off the oven and, to prevent cracking, leave the cheesecake inside with the oven door slightly ajar for about 30–60 minutes. This gradual cooling helps the center finish setting without a sudden chill. Then remove from oven.
Chill in refrigerator. Transfer the mini cheesecakes (still in their pans) to the fridge. Chill for at least 1–2 hours, or better yet overnight for a firmer texture. Proper chilling allows the flavors to meld and the cheesecakes to fully set.
Serve. Once chilled, top each mini cheesecake with your favorite keto-friendly topping: fresh berries, sugar-free whipped cream, or a drizzle of melted sugar-free chocolate. Run a thin knife around the edges to release, then unmold. Enjoy each mini cake cold or slightly warmed.
Store leftovers. Cover any leftovers with plastic wrap or keep in an airtight container in the fridge. They stay fresh for up to 5–7 days. (You can also freeze individual portions for up to a month and thaw in the fridge before serving.)

Nutritional Breakdown

While exact nutrition depends on your ingredient brands and portioning, here is the approximate macro per mini cheesecake (recipe makes 4 6-oz servings):

Calories: ~160–250 kcal (depending on crust thickness)
Total carbs: 3–6 g (almost all from the dairy; almond flour adds fiber)
Fiber: ~1–2 g (mostly from almond flour)
Net carbs: ~2–4 g
Protein: ~10 g
Fat: ~12–22 g (healthy fats from cream cheese, eggs, butter, and almond flour)

For example, one mini cheesecake (as calculated by the recipe at Sugar-Free Mom) contains about 161 calories, 3 g carbs, and 10 g protein. The almond-flour crust adds some fat and fiber without many net carbs, keeping the macros keto-friendly. Overall this is a high-protein, low-carb dessert – much more protein than a traditional cheesecake.

Nutrient Highlights: Cottage cheese is a powerhouse of protein and nutrients. A ½-cup serving alone gives around 12–15 g protein and just ~4–5 g carbs. Combined with eggs (each egg has ~6 g protein) and full-fat dairy, these mini cheesecakes pack a muscle-supporting punch. The high protein content also helps you feel full longer and stabilizes blood sugar – benefits noted in studies for weight management and muscle health. The fats from butter, almond flour, and dairy provide steady energy for keto metabolism.

Variations

Lemon Berry Cheesecakes: Add a fresh twist by making this a lemon or berry cheesecake. For a lemon version, stir in the zest of 1 lemon and 1–2 tablespoons lemon juice into the batter before baking. Serve topped with a dollop of sugar-free lemon curd or extra lemon zest. For a berry version, gently fold a handful of mashed fresh or thawed frozen berries (strawberries, raspberries, or blueberries) into the filling before baking. The tart berry juices will color the batter light pink/purple. Alternatively, bake plain and top each mini cake with fresh berries and a sprinkle of almond flour crumbs. Both variations add flavor without many extra carbs. (Berries contain some carbs, so account for those if counting strictly – but used sparingly, they fit keto well.)
No-Crust Cheesecake: You can skip the crust entirely if you prefer. Simply pour the filling into greased ramekins or silicone molds and bake as directed. You’ll have a crustless cottage cheese cheesecake that’s even lower in carbs (and calories). It will slice like a soft custard rather than a crumbly cake. Serve with berries or whipped cream.
Nutty Variations: Swap half the almond flour for finely chopped walnuts or pecans for a different crust flavor. You could also use pecan meal or even a mix of almond/coconut flours (reduce coconut flour significantly, as it absorbs more liquid).
Chocolate Cheesecake: For a chocolate twist, add 2 tablespoons unsweetened cocoa powder to the filling mixture and increase sweetener if needed. Top with keto chocolate shavings or sugar-free chocolate sauce after baking.
Swirled Cheesecake: Reserve a few tablespoons of the plain filling. Mix it with 1–2 tablespoons sugar-free berry jam or melted sugar-free chocolate, then spoon dollops of each batter into the pan and swirl with a toothpick for a pretty pattern.

Tips for Success

Strain the cottage cheese: For the creamiest texture, line a sieve with cheesecloth and drain the cottage cheese before blending. Removing excess whey (liquid) prevents a runny filling and yields a silkier cheesecake.
Room-temperature ingredients: Let the cottage cheese, cream cheese, sour cream, and eggs come to room temperature before mixing. This makes for a smoother batter. Cold cream cheese can clump.
Don’t overmix after eggs: Once the eggs are added, blend just until incorporated. Over-mixing after adding eggs can whip too much air into the batter, causing cracks.
Water bath: Placing the cheesecake pan in a pan of hot water (water bath) while baking helps it cook evenly and prevents cracking. The moisture keeps the edges from drying out.
Don’t overbake: The cheesecake is done when the edges are set and the center still jiggles slightly. The filling will continue to firm as it cools. Overbaking can make it dry or cause large cracks.
Gradual cooling: To avoid cracks, let the cheesecake cool slowly. Turn off the oven when done and crack the door open slightly, letting the cake sit in the warm oven for 30–60 minutes. This prevents a sudden temperature change.
Chill thoroughly: For the best texture and flavor, chill the baked cheesecakes in the fridge for a few hours or overnight. Well-chilled cheesecake slices cleanly and tastes more cohesive.
Cut with care: Use a hot, sharp knife for clean slices. Wipe the knife between cuts.

FAQs

Q: Can I use low-fat cottage cheese or Greek yogurt?
A: Yes. Using low-fat cottage cheese will reduce the fat content but increase relative carbs (some low-fat versions have slightly more carbs and thickeners). It will still work, though the texture may be a bit less rich. Greek yogurt (full-fat) can also be substituted; it will produce a creamier taste but slightly less protein. If using Greek yogurt, ensure it’s unsweetened and full-fat to keep it keto-friendly.

Q: What if I don’t have almond flour?
A: You can use other nut flours like coconut flour, but the substitution isn’t 1:1. Coconut flour absorbs much more liquid (about ¼ cup coconut flour per cup almond flour) and changes the texture. A simple fix: make a coconut flour crust by mixing ½ cup coconut flour, 4 tbsp butter, and a bit of sweetener (you may need an extra egg white in the filling to help set). Alternatively, use hazelnut flour or a mix of almond meal and finely chopped nuts. Just know that coconut flour has very little fat, so your crust will be drier.

Q: Can I make this ahead or freeze it?
A: Absolutely. These mini cheesecakes can be made a day in advance – in fact, they taste better after resting. Store them in the fridge (covered) for up to 5–7 days. To freeze, wrap each cheesecake well (removable from ramekin) and store in a freezer-safe container. Thaw in the fridge when ready to enjoy; texture will be almost as good as fresh.

Q: Can I double the recipe?
A: Yes. You can easily double the ingredients to make 8 mini cheesecakes or one larger pan (e.g. a 6-inch or 8-inch cake). Just bake longer – a larger 6-inch springform (double recipe) will take about 40 minutes. Check for doneness by looking for slight jiggle in center.

Q: How do I prevent cracks?
A: Follow the gentle bake and cooling tips above. Room-temp ingredients, not overbaking, and gradual cooling are key. The cottage cheese adds moisture and elasticity to the filling, which also helps prevent cracks compared to a classic cheesecake. The water bath trick is very effective – it stops the outside from cooking too much faster than the center.

Disclaimer

Some links in this post are affiliate links, which means I may earn a small commission if you make a purchase through them (at no extra cost to you). I only recommend products I trust and use myself. All opinions here are my own.