Make the blueberry layer: Add blueberries, sweetener, lemon zest, and lemon juice to a small saucepan over medium heat. Stir until the berries release juices and start to burst, 4–6 minutes.
Lightly mash to your preferred texture. Stir in chia seeds if using. Cool to room temperature.
Mix the crust: In a bowl, combine almond flour, melted butter, sweetener, cinnamon, and salt.
Stir until it resembles damp sand and clumps lightly. Set aside.
Prepare the cheesecake filling: In a mixing bowl, beat softened cream cheese with sweetener and salt until smooth. Add Greek yogurt and vanilla, then beat until creamy.
Sprinkle in protein powder and mix just until incorporated and silky. Taste and adjust sweetness.
Assemble the jars: Spoon 1–2 tablespoons of crust into the bottom of each jar and press gently. Add a layer of cheesecake filling (about 1/3–1/2 cup).
Top with a spoonful of blueberry compote. Repeat layers if your jars allow, finishing with blueberries.
Chill: Cover and refrigerate for at least 1–2 hours to set and marry the flavors. For the best texture, chill 4 hours or overnight.
Serve: Enjoy straight from the jar.
Add a few fresh blueberries or a dusting of cinnamon on top if you like.