Preheat the oven to 350°F (175°C) and line a 12-cup muffin tin with cupcake liners.

In a medium bowl, whisk together the almond flour, cocoa powder, powdered keto-friendly sweetener, baking powder, baking soda, and salt, making sure there are no large lumps of cocoa or almond flour.

In a separate bowl, whisk the eggs gently, then add the melted and slightly cooled butter, unsweetened almond milk, vanilla extract, apple cider vinegar, and enough red food coloring to achieve the desired red color.

Gradually add the dry ingredients to the wet ingredients, stirring gently until a smooth, thick batter forms. Stop mixing as soon as there are no visible dry ingredients to avoid creating a dense cupcake.

Divide the batter evenly between the 12 cupcake liners, filling each approximately two-thirds full so the cupcakes have enough room to rise without overflowing.

Bake for 18–22 minutes, checking around 18 minutes. Insert a toothpick into the center of one cupcake; it should come out with a few moist crumbs but no wet batter.

Remove the cupcakes from the oven and let them cool in the muffin tin for 5–10 minutes before transferring them to a wire rack. Allow them to cool completely before adding the filling.

Wash and thoroughly dry the strawberries. Remove the tops and finely chop them or pulse them briefly in a food processor. If they are especially juicy, blot them gently with paper towels to remove excess moisture.

Beat the softened cream cheese until completely smooth. Add the powdered sweetener, vanilla extract, and heavy cream, then mix until creamy and thick.

Add the prepared strawberries to the cream cheese mixture and mix until the strawberry pieces are evenly distributed. If the filling seems too soft to pipe, refrigerate it for 15–20 minutes.

Use a small sharp knife to carefully cut a small circular cavity from the center of each cooled cupcake. Do not cut all the way through to the bottom, and save the removed cake pieces for snacking or another dessert.

Spoon or pipe the strawberry cheesecake filling into each cupcake cavity, filling it generously without pressing down hard enough to compress the cupcake.

For the topping, beat the softened cream cheese until smooth, then add the powdered sweetener and vanilla extract. Gradually add the heavy cream and mix until the frosting reaches a smooth, pipeable consistency.

Pipe or spread a small amount of cream cheese frosting over each filled cupcake. Keep the topping moderate because the strawberry cheesecake center already provides plenty of creamy richness.

If desired, garnish each cupcake with a small strawberry slice, crushed freeze-dried strawberries, chopped pecans, or a light drizzle of keto-friendly chocolate.

Refrigerate the finished cupcakes for 30–60 minutes before serving so the cheesecake center can firm up. Serve chilled or let individual cupcakes sit at room temperature for approximately 10 minutes for a softer texture.