Bioactive peptides are present in all living organisms and have critical roles ranging from protection against infection as the key element of innate immunity, regulating blood pressure and glucose levels, to reducing signs of ageing by killing senescent cells. Bioactive peptides are also encrypted within food protein sequences that can be released during proteolysis or food processing. These specific food protein fragments are reported to have potential for improving human health and preventing metabolic diseases through their impact on inflammation, blood pressure, obesity, and type-2 diabetes. This review mainly focuses on the molecular targets and the underlying mechanisms of bioactive peptides against various metabolic syndromes including inflammation, high blood pressure, obesity, and type-2 diabetes, to provide new insights and perspectives on the potential of bioactive peptides for management of metabolic syndromes.