One of the main objectives of present and future space exploration missions dedicated to astrobiology is the detection of organic molecules of interest for life (e.g. amino and fatty acids). With this aim, a sample preparation and a gas chromatograph (connected to a mass spectrometer) are generally used. To date, tetramethylammonium hydroxide (TMAH) has been the first and only thermochemolysis reagent to be used for in situ sample preparation and chemical analysis of planetary environments. Although TMAH is widely used in terrestrial laboratories, numerous applications also leverage other thermochemolysis reagents that may be more relevant than TMAH to meet both scientific and technical objectives of space instrumentation. The present study compares the performance of tetramethylammonium hydroxide (TMAH), trimethylsulfonium hydroxide (TMSH), and trimethylphenylammonium hydroxide (TMPAH) reagents on molecules of interest to astrobiology. The study focuses on the analyses of 13 carboxylic acids (C7–C30), 17 proteinic amino acids, and the 5 nucleobases. Here we report the derivatization yield without stirring or adding solvents, the detection sensitivity with mass spectrometry, and the nature of the degradation products from the reagents produced during pyrolysis. We conclude that TMSH and TMAH are the best reagents for analyzing carboxylic acids and nucleobases. Amino acids are not relevant targets for a thermochemolysis over 300 °C as they are degraded and showed high limits of detection. As TMAH, and probably TMSH, meet the space instrumentation requirements, this study informs sample treatment approaches prior to GC-MS analysis in in situ space studies. The thermochemolysis reaction using TMAH or TMSH is also recommended for space return missions to extract organics from a macromolecular matrix, derivatize polar or refractory organic targets, and volatilize with the fewest organic degradations.