Combine protein powder, collagen, almond flour, cocoa powder, salt, and monk fruit in a food processor.
In a small bowl, stir together the water, extracts, and color, if using.
With the food processor running, stream the water mixture in. Process until the batter comes together in a large ball. Add water a tablespoon at a time and process well to ensure it is incorporated before adding more if it seems too dry.
Break the cream cheese into large pieces and press into the protein bar dough and knead slightly to swirl the cream cheese throughout. Press into an 8×8-inch pan lined with parchment or plastic wrap.
Refrigerate until cool and set, about an hour, slice into 12 bars and wrap individually with parchment paper. Store in the refrigerator until eating as they can spoil. These can be taken for travel and will not melt although they will get quite soft and tacky when warm.