An overlay metrology system includes an overlay metrology tool configurable to generate overlay signals with a plurality of recipes and further directs an illumination beam to an overlay target and collects radiation emanating from the overlay target in response to the at least a portion of the illumination beam to generate the overlay signal with the particular recipe. The overlay metrology system further acquires two or more overlay signals for a first overlay target using two or more unique recipes, subsequently acquires two or more overlay signals for a second overlay target using the two or more unique recipes, determines candidate overlays for the first and second overlay targets based on the two or more overlay signals for each target, and determines output overlays for the first and second overlay targets based on the two or more candidate overlays for each target.