Abstract: There are provided systems, methods, and processor-readable media for optimizing the end to end operation of a hydrocarbon processing system using NMR spectroscopy data. The hydrocarbon processing system is configured to process hydrocarbon feedstock material, via a configuration defined by a set of configuration parameters, such that one or more final products are produced. A yield prediction model is used to process NMR data obtained from an NMR scan of the feedstock material to generate yield prediction data. The yield prediction data includes predictions of product yields of various intermediate products and/or final products. An optimization module is used to process the yield prediction data predicted by the trained yield prediction model such that optimized configuration parameter data is obtained. The optimized configuration parameter data is effective for establishing an optimized configuration for operating the hydrocarbon processing system that optimizes or improves an objective metric.