Prep the pan and oven: Heat the oven to 325°F (163°C).
Line the bottom of a 9-inch springform pan with parchment. Lightly grease the sides.
Mix the dry brownie ingredients: In a bowl, whisk oat or almond flour, cocoa powder, sugar/sweetener, baking powder, and salt until no clumps remain.
Add the wet ingredients: Whisk in eggs, milk, oil, and vanilla until smooth and glossy. Fold in chocolate chips if using.
Par-bake the brownie base: Spread the batter evenly in the pan.
Bake for 12–14 minutes, until set around the edges but soft in the center. Set aside while you make the cheesecake.
Beat the cream cheese: In a mixing bowl, beat cream cheese on medium speed for 1–2 minutes until fluffy and smooth. Scrape the bowl.
Add yogurt, sugar, and protein: Mix in Greek yogurt, sugar/sweetener, protein powder, vanilla, lemon juice, and salt.
Beat on low, then medium, until smooth. Avoid overmixing.
Add the eggs: Beat in eggs one at a time on low speed, just until incorporated. Scrape the bowl to prevent lumps.
Combine layers: Pour the cheesecake batter over the warm brownie base.
Tap the pan on the counter to release any air bubbles.
Bake low and slow: Bake at 325°F (163°C) for 35–45 minutes. The edges should be set and the center should jiggle slightly like gelatin. If browning too quickly, tent loosely with foil.
Cool gradually: Turn off the oven, crack the door, and let the cheesecake rest inside for 20 minutes.
Then cool at room temperature for 1 hour.
Chill overnight: Cover and refrigerate at least 6 hours, preferably overnight, for the best texture and clean slices.
Slice and serve: Run a thin knife around the edge, release the springform, and cut with a hot, clean knife. Wipe between cuts for tidy slices.