Climate change is expected to increase the frequency and severity of abiotic stresses (e.g., hot spell, salinity, drought), which might lead to loss of crop yield. We investigated the effect of salinity (S), short episodes of high temperature (HS) and combination of S+HS at the reproductive phase on seeds and dead pericarps properties of the crop plant Brassica juncea. Three interval exposures to HS resulted in massive seed abortion, and seeds from salt-treated plants germinated poorly. HS significantly reduced metabolites accumulated in dead pericarps, except for upregulation of isomaltose and cellobiose. Salt induced alteration in metabolite levels including increase in proline, reduction in TCA intermediates and changes in phytohormone levels. Proteome analysis revealed hundreds of proteins stored in dead pericarps whose levels and composition were altered under salt stress. The integration of metabolic and proteomic data showed that changes in metabolites were highly correlated with changes in proteins involved in their biosynthetic pathways. Thus, dead pericarps store beneficial substances whose level and composition are altered under stress conditions. The results highlighted the detrimental effect of short episodes of HS during the reproductive phase on crop production, which might have implications for global food security in the face of climate change.