Pathogens get entry into host cell, reproduce there and use biological machinery of host plants which is threat to global crop production. Integrated management strategies based upon minimizing population and use of resistant cultivars can address this potential problem. In developing world farmers are less likely to adopt these approaches instead they prefer the use of chemical pesticides. Reckless use of chemical pesticides is destroying our ecosystem. That's why it is required to explore ecofriendly alternatives, like plant based metabolites to control pathogens. Studies conducted on different plant-metabolites reported that these metabolite can potentially combat plant pathogens. In this study we have also discussed some of plant secondary metabolites including alkaloids, flavonoids and phenolics. In this review we tried to highlight the new trends in utilizing secondary metabolites for controlling bacterial, viral and fungal pathogens with the hope that upcoming drugs will be human and ecosystem friendly. •Plants synthesize diversity of secondary metabolites.•Secondary metabolites prominently functions to protect plant.•Secondary metabolites induced against microbes and insects attack.•We have highlight the new trends in utilizing secondary metabolites for controlling bacterial, viral and fungal pathogens and insects.