The trade-off between protein and oil storage in oilseed crops has been tested here in oilseed rape (Brassica napus) by analyzing the effect of suppressing key genes encoding protein storage products (napin, cruciferin). The phenotypic outcomes were assessed using magnetic resonance and mass spectrometry imaging, microscopy, transcriptomics, proteomics, metabolomics, lipidomics and immunological assays. Surprisingly, the storage product profile of the seeds of RNAi transgenics was rather moderately changed, but embryonic cells underwent remarkable architectural rearrangements. The most conspicuous structural changes featured the elaboration of membrane stacks enriched with oleosin (6-fold higher protein abundance). Protein rebalancing, amino acid and sulfur metabolism were focal points of the metabolic adjustments to maintain the carbon/nitrogen homeostasis of embryo. Flux balance analysis was evident for a rather minor additional demand for cofactors (ATP, NADPH). The conclusion was that cellular plasticity in the seed provides a buffer that protects against perturbations to its storage activity, and hence contributes materially to the homeostasis required to assure successful sexual reproduction. The study provides novel mechanistic insights into the intriguing linkage between lipid and protein storage, which have implications for biotechnological strategies directed at the improvement of oilseed crops.