Practice
On return to Edinburgh he set up in surgical practice and within a year, at the age of 24, was elected one of four attendant surgeons to the Royal Infirmary of Edinburgh. Surgeons attended in rotation and Bell managed to remain a surgeon to the Infirmary for eighteen years, an unusually long period. This may have been because of his lifelong friendship with James Gregory, the Professor of Physic, and the most influential member of the Infirmary Board of Management. In 1800 there was pressure from younger members of the Royal College of Surgeons to change the system of appointment of surgeons to the Infirmary, making shorter appointments so that more junior surgeons might gain Infirmary experience. At that time, now well established in practice, Bell was content to step down, but he wrote to the College setting out the case for 'permanent appointments' to the Infirmary rotation, a view which had been also promoted by Gregory. Of the 23 members of the Royal College of Surgeons asked to vote on the matter, not one supported Bell's proposal. John Bell (1763–1820), a successful teacher of anatomy in his own extramural school and an accomplished Edinburgh surgeon (but not related to Benjamin Bell), failed to gain appointment to the Infirmary rota, and began to campaign against what he saw as the injustice of the rota system. As part of this he wrote criticising Gregory's views, and this brought the Bells, Benjamin and John into conflict. This feud was at the heart of much of the criticism to which Benjamin Bell was subjected by his namesake.
In 1773 Bell was a founding member of the Aesculapian Club. In 1775 Bell fell from horseback and sustained injuries that were to force him to take a rest from surgical practice for some two years. This rest was to prove fortuitous, for it allowed him time to reflect and to write, and his relatively wealthy background enabled him to do this without financial concerns. To further develop his interest in farming during this period of recuperation, he took the lease of Liberton Farm situated some two miles south of the centre of Edinburgh.
Returning to what was to prove a highly successful career as a surgeon in Edinburgh, Bell went into practice with James Gibson (died 1815) who was to become president of the Royal College of Surgeons of Edinburgh in 1778–79. Later he formed another surgical partnership with James Russell (1754–1836) and Andrew Wardrop (died 1823). Bell, Wardop and Russell became the leading surgical practice in Scotland with a wide referral base. Wardrop reckoned Bell "… was a successful operator and during many years was more employed than any surgeon in Scotland". A fellow surgeon John Campbell, who had been apprenticed to Bell, went so far as to suggest that "…no one could die contented without having consulted Benjamin Bell."
On 12 April 1782 Bell was one of the founding members of the Harveian Society of Edinburgh and served as President in 1792. On 17 November 1783 he was one of the founding Fellows of the Royal Society of Edinburgh.
He died at Newington House in south Edinburgh. He is buried with other family members, including his wife Grizzel Hamilton, in the south-east corner of Canongate Churchyard in Edinburgh.