He is perhaps most widely remembered for his pioneering work in Portugal in the field of anaesthesiology, as the first physician in the country to use chloroform in a surgical procedure (on 12 January 1848, during a knee tumorectomy); he is also credited with the popularization of the use of creosote and of the first ether inhalers.

[1] At the invitation of the Marquis of Palmela, who was part of the Liberal government-in-opposition, Bernardino António Gomes rejoined the Liberal forces in Terceira Island in the Azores: he would later take part in the Landing at Mindelo, the turning point of the Civil War, and was in the besieged resistance at the Siege of Porto (during which he provided medical assistance due to a cholera outbreak).

He was sent as a national delegate to the third of the International Sanitary Conferences (in Constantinople, 1866); in opposition to Pettenkofer's anti-contagionism that dominated the scientific thinking of the conference, Bernardino António Gomes was a staunch defender of the theory of contagion and considered it advisable to ban all maritime communication to quell the ongoing cholera pandemic that had begun in the Ganges Delta, "to combat the scourge in the very countries in which it is born or, at least, to halt its progress as near as possible to its original home" (measures that were opposed, notably, by the delegates from the United Kingdom).

[4][5] In 1858, Bernardino António Gomes became embroiled in a heated pamphlet war with the Duke of Saldanha, one of the leading promoters of homeopathy and other systems of alternative medicine like mesmerism or the "Raspail method" in the country.

[8] As a natural historian, Bernardino António Gomes published an exhaustive review of the fossil flora of the Carboniferous systems in Portugal (1865), and was a contributor in the Catalogus Plantarum Horti Botanici Medico-Cirurgicae Scholae Olisiponensis (1851).