Keto Blueberry Cheesecake Muffins – Creamy, Fruity, and Low-Carb

These Keto Blueberry Cheesecake Muffins bring together the best of both worlds: the fluffiness of a muffin and the creamy richness of cheesecake. They’re sweet without sugar, satisfying without the carbs, and bursting with juicy blueberries in every bite. Whether you’re watching your macros or just want a lighter treat, these muffins hit the spot.

They’re perfect for breakfast, snacks, or a little dessert after dinner. You’ll love how easy they are to make and how well they hold up for meal prep.

Keto Blueberry Cheesecake Muffins - Creamy, Fruity, and Low-Carb

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Prep Time 15 minutes mins

Cook Time 20 minutes mins

Total Time 35 minutes mins

Servings: 12 servings

Ingredients Method

Ingredients

  

• For the muffin batter:
• 2 cups almond flour (finely blanched)
• 2 tablespoons coconut flour
• 2 teaspoons baking powder
• 1/4 teaspoon fine sea salt
• 1/2 cup granular erythritol or monk fruit blend (adjust to taste)
• 1/2 cup unsalted butter, melted and cooled (or refined coconut oil)
• 3 large eggs, room temperature
• 1 teaspoon vanilla extract
• 1/3 cup unsweetened almond milk (more as needed for consistency)
• 3/4 cup blueberries (fresh or frozen; if frozen, do not thaw)
• 1 teaspoon lemon zest (optional, but brightens flavor)
• For the cheesecake swirl:
• 8 ounces cream cheese, softened
• 1/4 cup powdered erythritol or monk fruit blend
• 1 large egg yolk
• 1/2 teaspoon vanilla extract
• 1 teaspoon lemon juice (optional)
• For the pan:
• Muffin liners and a light spray of avocado oil or butter

Method

 

1. Prep your pan and oven: Line a 12-cup muffin tin with liners and lightly grease them. Preheat the oven to 350°F (175°C).
2. Mix dry ingredients: In a medium bowl, whisk almond flour, coconut flour, baking powder, salt, and granular sweetener until well combined.
3. Combine wet ingredients: In a large bowl, whisk melted butter, eggs, vanilla, and almond milk. Add lemon zest if using.
4. Make the muffin batter: Add the dry mix to the wet ingredients and stir until just combined. If the batter seems too thick, add 1–2 tablespoons more almond milk. Gently fold in the blueberries.
5. Make the cheesecake mixture: In a separate bowl, beat cream cheese with powdered sweetener until smooth. Mix in egg yolk, vanilla, and lemon juice until creamy.
6. Fill the cups: Spoon about 2 tablespoons of muffin batter into each liner, then add 1 tablespoon of cheesecake mixture on top. Finish with another tablespoon of muffin batter. Swirl gently with a toothpick.
7. Bake: Bake for 20–24 minutes, or until the tops are set and lightly golden and a toothpick inserted into the muffin portion comes out mostly clean. The cheesecake centers will be slightly soft.
8. Cool completely: Let the muffins cool in the pan for 10 minutes, then move to a rack. Chill for 30–60 minutes for the creamiest texture.
9. Serve: Enjoy chilled or at room temperature. The flavor deepens after a few hours.

Why This Recipe Works

• Balanced texture: A tender almond flour base pairs with a creamy cheesecake swirl for a bakery-style bite.
• Low-carb ingredients: Almond flour, cream cheese, and a keto-friendly sweetener keep carbs in check without sacrificing flavor.
• Blueberry boost: Fresh or frozen blueberries add natural sweetness and moisture without spiking carbs too much.
• Easy method: Two quick batters, one pan, and simple steps make this weeknight-friendly.
• Make-ahead friendly: These muffins store well and taste even better the next day.

Ingredients

• For the muffin batter:
• 2 cups almond flour (finely blanched)
• 2 tablespoons coconut flour
• 2 teaspoons baking powder
• 1/4 teaspoon fine sea salt
• 1/2 cup granular erythritol or monk fruit blend (adjust to taste)
• 1/2 cup unsalted butter, melted and cooled (or refined coconut oil)
• 3 large eggs, room temperature
• 1 teaspoon vanilla extract
• 1/3 cup unsweetened almond milk (more as needed for consistency)
• 3/4 cup blueberries (fresh or frozen; if frozen, do not thaw)
• 1 teaspoon lemon zest (optional, but brightens flavor)
• For the cheesecake swirl:
• 8 ounces cream cheese, softened
• 1/4 cup powdered erythritol or monk fruit blend
• 1 large egg yolk
• 1/2 teaspoon vanilla extract
• 1 teaspoon lemon juice (optional)
• For the pan:
• Muffin liners and a light spray of avocado oil or butter

How to Make It

1. Prep your pan and oven: Line a 12-cup muffin tin with liners and lightly grease them. Preheat the oven to 350°F (175°C).
2. Mix dry ingredients: In a medium bowl, whisk almond flour, coconut flour, baking powder, salt, and granular sweetener until well combined.
3. Combine wet ingredients: In a large bowl, whisk melted butter, eggs, vanilla, and almond milk.

   Add lemon zest if using.

4. Make the muffin batter: Add the dry mix to the wet ingredients and stir until just combined. If the batter seems too thick, add 1–2 tablespoons more almond milk. Gently fold in the blueberries.
5. Make the cheesecake mixture: In a separate bowl, beat cream cheese with powdered sweetener until smooth.

   Mix in egg yolk, vanilla, and lemon juice until creamy.

6. Fill the cups: Spoon about 2 tablespoons of muffin batter into each liner, then add 1 tablespoon of cheesecake mixture on top. Finish with another tablespoon of muffin batter. Swirl gently with a toothpick.
7. Bake: Bake for 20–24 minutes, or until the tops are set and lightly golden and a toothpick inserted into the muffin portion comes out mostly clean.

   The cheesecake centers will be slightly soft.

8. Cool completely: Let the muffins cool in the pan for 10 minutes, then move to a rack. Chill for 30–60 minutes for the creamiest texture.
9. Serve: Enjoy chilled or at room temperature. The flavor deepens after a few hours.

How to Store

• Refrigerator: Store in an airtight container for up to 5 days.

  Keep a paper towel under the lid to absorb moisture.

• Freezer: Freeze in a single layer, then transfer to a freezer bag. Keeps well for up to 2 months. Thaw overnight in the fridge.
• Reheat: Enjoy cold, or warm briefly in the microwave for 10–15 seconds to soften.

Benefits of This Recipe

• Keto-friendly macros: Low net carbs with satisfying fat and moderate protein.
• Gluten-free: Almond and coconut flours replace wheat flour without sacrificing texture.
• Portion-controlled: Individual muffins help you manage servings with ease.
• Meal prep ready: They store and freeze well, making weekday breakfasts simple.
• Versatile flavor: The blueberry-lemon-cheesecake combo feels special but suits any occasion.

Common Mistakes to Avoid

• Overmixing the batter: Almond flour batters can turn dense.

  Stir until just combined.

• Using too much liquid: Keto batters should be thick. Add almond milk slowly for a scoopable texture.
• Skipping the liners: These muffins are tender and can stick. Liners make removal easy and clean.
• Overbaking: Cheesecake dries out quickly.

  Pull them when the tops are set and edges are lightly golden.

• Thawing frozen blueberries: Use them straight from the freezer to avoid purple-streaked batter.

Alternatives

• Sweetener swaps: Use your favorite keto sweetener. For a smoother cheesecake layer, choose a powdered blend.
• Dairy-free option: Use dairy-free cream cheese and coconut oil instead of butter. Texture will differ slightly but still delicious.
• Flavor twist: Swap blueberries for raspberries or blackberries, or add 1/2 teaspoon almond extract for a bakery vibe.
• Topping ideas: Sprinkle unsweetened shredded coconut, sliced almonds, or a few extra blueberries before baking.
• Nut-free version: Replace almond flour with a seed-based baking blend made for low-carb recipes.

  Avoid straight coconut flour as a 1:1 swap—it’s too absorbent.

FAQ

Are blueberries keto-friendly?

Small amounts of blueberries fit well into a keto diet. This recipe uses a modest portion spread across 12 muffins, keeping net carbs per serving reasonable.

Can I make these without coconut flour?

Yes, but you’ll need to increase almond flour slightly to maintain structure. Start by adding 2–3 more tablespoons of almond flour and adjust with a splash of almond milk if needed.

What’s the best sweetener for this recipe?

A monk fruit–erythritol blend works well for the muffin batter.

Use a powdered version in the cheesecake layer for a smooth finish without grit.

How do I keep the muffins from sticking?

Use quality muffin liners and lightly grease them. Let muffins cool before removing, and chill briefly if they feel delicate.

Can I make mini muffins?

Yes. Use a mini muffin pan and reduce the bake time to about 12–15 minutes.

Keep the cheesecake dollops small so they set properly.

How many carbs are in each muffin?

Exact numbers depend on your brands and portion sizes. As a ballpark, each muffin typically lands around 3–5g net carbs when made as written.

Do I have to chill them before eating?

You can eat them warm, but chilling firms up the cheesecake layer and gives a cleaner bite. The flavor also improves after a short rest.

Can I use frozen blueberries?

Absolutely.

Don’t thaw them. Fold them in frozen to prevent excess moisture and color bleed.

What if my cheesecake layer is lumpy?

Make sure your cream cheese is fully softened and use powdered sweetener. Beat until smooth before adding the egg yolk.

Can I make them ahead for guests?

Yes.

Bake the day before, chill overnight, and serve the next day. They hold up beautifully and taste even better.

Wrapping Up

Keto Blueberry Cheesecake Muffins deliver creamy, fruity comfort in a low-carb package. They’re simple to bake, easy to store, and flexible enough for different diets and flavors.

Whether you want a grab-and-go breakfast or a sweet treat that won’t derail your goals, this recipe has you covered. Make a batch today, and enjoy a bakery-style bite without the sugar crash.