Methods and systems for detecting and correcting substrate process drift using machine learning are provided. Data associated with processing each of a first set of substrates at a manufacturing system according to a process recipe is provided as input to a trained machine learning model. One or more outputs are obtained from the trained machine learning model. An amount of drift of a first set of metrology measurement values for the first set of substrates from a target metrology measurement value is determined from the one or more outputs. Process recipe modification identifying one or more modifications to the process recipe is also determined. For each modification, an indication of a level of confidence that a respective modification to the process recipe satisfies a drift criterion for a second set of substrates is determined. In response to an identification of the respective modification with a level of confidence that satisfies a level of confidence criterion, the process recipe is updated based on the respective modification.