Compared with other ocean basins, little is known scientifically about the seamounts in the Indian Ocean. Nonetheless, fishers have plundered these fragile ecosystems for decades, and now mining is becoming a reality. We introduce a multidisciplinary project referred to as MADRidge that recently focused on three shallow seamounts in the South West Indian Ocean between 19°S and 34°S. The larger Walters Shoal (summit at 18 m) discovered in 1963 occupies the southern part of the Madagascar Ridge and has long received attention from the fishing industry, and only recently by scientists. In contrast, nothing is known of the northern region of the ridge, which is characterised by a prominent, steep-sided seamount that has a flat circular summit at 240 m and width of ∼20 km. This seamount is some 200 km south of Madagascan and unnamed; it is referred to here as the MAD-Ridge seamount. MAD-Ridge is the shallowest of a constellation of five deeper (>1200 m) seamounts on that part of the ridge, all within the EEZ of Madagascar. It lies in a highly dynamic region at the end of the East Madagascar Current, where mesoscale eddies are produced continuously, typically as dipoles. The Madagascar Ridge appears to be an area of great productivity, as suggested by the foraging behaviour of some tropical seabirds during chick-rearing and a longline fishery that operates there. The third seamount, La Pérouse, is located between Réunion Island and Madagascar. With a summit 60 m below the sea surface, La Pérouse is distinct from MAD-Ridge and Walters Shoal; it is a solitary pinnacle surrounded by deep abyssal plains and positioned in an oligotrophic region with low mesoscale activities. The overall aim of the MADRidge project was to examine the flow structures induced by the abrupt topographies, and to evaluate whether biological responses could be detected that better explain the observed increased in fish and top predator biomasses. The MADRidge project comprised a multidisciplinary team of senior and early career scientists, along with postgraduate students from France, South Africa, Mauritius and Madagascar. The investigation was based around three cruises using the French vessels RV Antea (35 m) and RV Marion Dufresne (120 m) in September 2016 (La Pérouse),November/December 2016 (MAD-Ridge) and May 2017 (Walters Shoal). This manuscript presents the rationale for the MADRidge project, the background, a description of the research approach including the cruises, and a synopsis of the results gathered in the papers published in this Special Issue.