Effect of malachite green toxicity on non target soil organisms

•Malachite green (MG) toxicity was tested on beneficial soil bacteria, fungi, earthworms and on seed germination of crop plants.•Genotoxicity, cytotoxicity and scanning electron microscopy assays concluded malachite green induced toxicity in soil microorganisms.•Filter paper and artificial soil test on earthworms demonstrated a LC 50 of 2.6mg/cm−2 and 1.45mg/kg respectively with evident morphological alterations.•Seed germination of Mung bean, Wheat and Mustard is unaffected in presence of MG upto 100ppm.•MG negatively effects growth, physiology of tested soil borne micro organisms and earthworms raising concerns about its environmental hazard.