Economically motivated adulteration (EMA) or misrepresentation of meat products is of concern, especially in developing countries, due to obvious health hazards and religious sensitivities. As Indian cooking involves prolonged heat treatments and addition of spices and condiments, species authentication of food, especially meat products, may be challenging. This study evaluated the efficacy of Polymerase Chain Reaction-Forensically Informative Sequencing (PCR-FINS) in meat speciation of highly processed meat. Further the prevalence of mislabelling in processed and deeply cooked meat products being sold in supermarkets and restaurants in a south Indian city was investigated. FINS targeting the mitochondrial cytochrome b gene and the ATP synthase gene was applied to identify meat species of 106 meat products labelled as chicken, beef, carabeef, mutton and pork. Mislabelling was detected in more than half of mutton (52.3%) and carabeef (55.5%), and in under a third (27.2%) of beef products. PCR-FINS is a reliable method for meat species identification even in highly processed food but there is a need for appropriate universal primers which can target all common species used in meat products. This study is the first of its kind from the South Indian state of Kerala.