Flavoromics aims to elucidate the molecules contributing to flavor perception by collecting as much chemical information as possible by adapting concepts and tools taken from the field of metabolomics. In this study, we have applied flavoromics to find markers of cooked and fermented flavor in strawberry juices submitted to different treatments (heat, storage, and freeze-drying). Chemical information from the samples was obtained by analysis of both volatile and non-volatile constituents, followed by processing of chromatograms and reduction in the number of variables using specialized software. By using Partial Least Squares Regression analysis, chemical data were correlated with the cooked and fermented flavor notes present in the strawberry juices (determined by sensory analysis). Some variables were selected as diagnostic markers, based on having a high impact in the statistical models developed. Regarding cooked flavor, most of the markers were chemical compounds known to be formed during heating of fruit juices; others were important volatile compounds of strawberries in their own right. On the other hand, the markers of fermented flavor were mainly esters, together with some alcohol oxides and compounds known generally for causing unpleasant flavor. The sensory contributions of these marker compounds will be further elucidated by targeted analysis and compound addition studies.