Allen was known in commerce for his pharmaceutical company at 2 Plough Court, trading in 1795 as Mildred & Allen while he was in partnership with Samuel Mildred. It was situated off Lombard Street in the City of London. In 1797, Allen brought in Luke Howard as a partner. A later partner was Daniel Bell Hanbury, father of the botanist Daniel Hanbury. By 1856, the company had become Allen & Hanburys. It was acquired in 1958 by Glaxo Laboratories, who retained the Allen & Hanburys name as a separate marque within the GSK group.