The Abrolhos shelf, in the eastern Brazilian margin, encompasses the largest reef province in the South Atlantic, characterised by low coral diversity and a high level of endemism. Knowledge gaps about how the Abrolhos coastal reefs evolved, during the post LGM and MIS 6/MIS 5, favoured a paradigm that is revisited in the light of new data. Here, new data from two new, long boreholes (20 and 50 m-long) are presented in order to investigate and provide new insights into the evolution of two shallow reefs on the Abrolhos Shelf during the late Pleistocene and Holocene epochs. Results show that Holocene and Pleistocene reefs grew on highly turbid waters with a significant terrigenous sediment input. Corals and CCA assemblages were identified as main framework builders of Abrolhos inner-shelf reefs since the Pleistocene. No clear shallowing upward sequence of reef builders was observed, which differs from other reef sequences all over the world. In terms of Holocene reef growth, Pedra Grande and Coroa Vermelha reefs turned on roughly coevally at different depths and with different coral assemblages. Pedra Grande reef started growing circa 6.8 kyr BP in a water depth approximately 10 m deeper than Coroa Vermelha, which started growing around 6.4 kyr BP, but Coroa Vermelha turned off at around 4 kyr BP, while Pedra Grande kept growing until around 1.2 kyr BP. This novel reef stratigraphy data provided a new insight on the evolution of the Abrolhos coastal reefs, showing that different environmental and topographic controls could have acted spatially in different ways. Coroa Vermelha reef seems to have started its growth as a result of a topographic high control. Pedra Grande reef seems to be connected to a broader submerged reef setting and started to grow in deeper water depths. The presence of three reef arcs in Abrolhos is proposed, including a submerged reef arc.