Drying fruits and vegetables is a long-established preservation method, and for tomatoes, in most cases sun-drying is preferred. Semi-drying is relatively a new application aimed to preserve better the original tomato properties. We have assessed the effects of different drying methods on the phytochemical variation in tomato products using untargeted metabolomics and targeted analyses of key compounds. An LC-MS approach enabled the relative quantification of 890 mostly semi-polar secondary metabolites and GC-MS analysis in the relative quantification of 270 polar, mostly primary metabolites. Metabolite profiles of sun-dried and oven-dried samples were clearly distinct and temperature-dependent. Both treatments caused drastic changes in lycopene and vi-tamins with losses up to > 99% compared to freeze-dried controls. Semi-drying had less impact on these com-pounds. In vitro bioaccessibility analyses of total phenolic compounds and antioxidants in a gastrointestinal digestion protocol revealed the highest recovery rates in semi-dried fruits. Semi-drying is a better way of pre-serving tomato phytochemicals, based on both composition and bioaccessibility results.