Methods and systems for improving a measurement recipe describing a sequence of measurements employed to characterize semiconductor structures are described herein. A measurement recipe is repeatedly updated before a queue of measurements defined by the previous measurement recipe is fully executed. In some examples, an improved measurement recipe identifies a minimum set of measurement options that increases wafer throughput while meeting measurement uncertainty requirements. In some examples, measurement recipe optimization is controlled to trade off measurement robustness and measurement time. This enables flexibility in the case of outliers and process excursions. In some examples, measurement recipe optimization is controlled to minimize any combination of measurement uncertainty, measurement time, move time, and target dose. In some examples, a measurement recipe is updated while measurement data is being collected. In some examples, a measurement recipe is updated at a site while data is collected at another site.