Prep the oven and pan: Preheat to 350°F (175°C).
Line a 12-cup muffin tin with paper liners or lightly grease with oil spray.
Whisk the dry mix: In a large bowl, whisk oat flour, almond flour, protein powder, cocoa powder, baking powder, baking soda, and salt until well combined and lump-free.
Blend the wet ingredients: In another bowl, whisk eggs, yogurt, almond milk, maple syrup, coconut sugar, oil, vanilla, vinegar, and beet puree until smooth. If using cream cheese for a swirl, keep it separate.
Combine gently: Pour the wet mixture into the dry. Stir with a spatula until just combined.
The batter should be thick but scoopable. Fold in chocolate chips if using. Do not overmix or the muffins will be dense.
Portion the batter: Divide evenly among the muffin cups, filling each about 3/4 full. For a cream cheese swirl, spoon 1/2 teaspoon on top of each muffin and use a toothpick to swirl.
Bake: Bake for 15–18 minutes, or until the tops spring back lightly and a toothpick comes out with a few moist crumbs (not wet batter).
Protein bakes can dry out fast, so start checking at 14 minutes.
Cool correctly: Let muffins cool in the pan for 5 minutes, then transfer to a wire rack to cool completely. This helps set the texture and prevents sogginess.
Taste and adjust: If you prefer a sweeter muffin, drizzle with a touch of warmed maple syrup or add a dusting of powdered erythritol before serving.