Faced with the challenges of adapting agriculture to climate change, seed production should have increased resilience to abiotic stress factors and the expected proliferation of pathogens. This concerns both the nutritional quality and seed vigor, two crucial factors in seedling establishment and yield. Both qualities are acquired during seed development, but how environment influences the genetic and physiological determinisms of these qualities remains to be elucidated. With a world production of 71 Mt of seeds per year, oilseed rape (Brassica napus) is the third largest oleaginous crop. But its productivity must cope with several abiotic stresses, among which drought is one of the main constraints in current and future climate scenarios. In addition, clubroot disease, caused by the pathogen Plasmodiophora brassicae, leads to severe yield losses for the Brassica crops worldwide. Clubroot provokes the formation of galls on the infected roots that can restrict the flow of water and nutrients within the plant throughout the growth cycle. In order to get new insights into the impact of single or combined constraints on seed qualities, metabolic profiling assays were run for a collection of 330 seed samples (including developing, mature and imbibed seeds) harvested from plants of two B. napus cultivars (“Express” and “Montego”) that were grown under either drought conditions, the presence of P. brassicae, or a combination of both stresses. Metabolites were identified and quantified by UPLC or GC. In addition, monitoring germination traits was conducted for 60 mature seed lots under in vitro conditions using an automated phenotyping platform. The present dataset contains the raw contents for 42 metabolites (nmol.mg-1 of seed dry weight) filtered and analyzed with statistical tests as well as germination speed and percentages. This dataset is available under accession at Data INRAE. These data will contribute to a better understanding of the crosstalk between the plant responses to water deprivation and/or pathogen attack and how it compromises seed quality. A better understanding of the molecular and physiological responses of the seed to (a)biotic stress on a molecular and physiological will be a first step to meet scientific and technological challenges of adapting seeds to their environment.