Seed performance is affected by the seed maturation environment and previously, we have shown that temperature, nitrate and light intensity were the most influential environmental factors affecting seed performance. Seeds developed in these environments were selected to assess the underlying metabolic pathways, using a combination of transcriptomics and metabolomics. These analyses revealed that the effects of the temperature and nitrate parental environments were reflected by partly overlapping genetic and metabolic networks, as indicated by similar changes in metabolites and transcripts expression levels. Nitrogen-metabolism related metabolites (asparagine, GABA and allantoin) were significantly decreased in both low temperature (15°C) and low nitrate (N0) maturation environments. Correspondingly, nitrogen-metabolism genes (ALLANTOINASE, NITRATE REDUCTASE 1, NITRITE REDUCTASE 1 and NITRILASE 4) were differentially regulated in the low temperature and nitrate maturation environments, as compared with control conditions. High light intensity during seed maturation increased galactinol content, and displayed a high correlation with seed longevity. Low light had a genotype-specific effect on cell surface encoding genes in the DELAY OF GERMINATION 6-Near Isogenic Line (NILDOG6). Overall, the integration of phenotypes, metabolites and transcripts led to new insights in the regulation of seed performance.