Heavy metal pollution has become a major constraint to crop yield and quality in the current times. These toxic metals amend various biochemical and physiological pathways and thus impose harmful effects on the growth and development of the plants. Nowadays, this situation has increased at an alarming rate and ultimately leads to food crisis in near future. To counter balance the heavy metal toxicity in plants, an in-depth understanding ranging from morphological to metabolome level is an essential step to improve crop yield. Recent advances in the omics technologies have assisted to unravel various metabolites/genes, stress proteins, ions and transcription factors and could be used as novel candidates to engineer plants tolerant to heavy metal stresses. Here we discuss the plant-heavy metal dynamic interactions in the light of omics era.