Introduction Camelina sativa is a Brassicaceae with interesting agronomic potential and is considered an alternative oilseed crop. Currently, Camelina is grown mainly for its seed, which shows a high oil content with an unusual fatty acid profile particularly rich in polyunsaturated fatty acids. Camelina seeds contain other potentially valuable compounds and their composition is now relatively well described. However, little information is available on the accumulation dynamics of these compounds during seed development. Objectives Our aim is to describe the dynamics of metabolites accumulation during C. sativa seed development. Methods After purification by HPLC, the fractions were analyzed by LC-MS and NMR to characterize new compounds. The dynamic of metabolites accumulation during seed development was monitored during 15, 25 and 35 days after flowering, and metabolic profilings were performed by LC-MS and GC-MS. Results This study describes for the first time two compounds (quercetin-5b-O-sinapyl-2 `'-O-apiosyl-3-O-rutinoside and epicatechin-7-O-glucose) that have not previously been identified in the seeds of C. sativa. We also show the accumulation kinetics of various metabolites involved in seed development. These investigations highlight a major reorganization of the metabolome with a depletion of the content of most primary metabolites and a high accumulation of most fatty acids, glucosinolates, flavonoids and sinapic acid derivatives. Conclusion This study resulted in the metabolic profile of C. sativa during seed development and enabled to identify two novel compounds in Camelina seeds.