Allen had concentrated on his own career in the field of pharmacy, taking over the Plough Court chemical business of Joseph Gurney Bevan who retired in 1795. In 1802, he was elected a Fellow of the Linnean Society and lectured on chemistry at Guy's Hospital. A year later he was made president of the Physical Society at Guy's, and on the advice of Humphry Davy and John Dalton also accepted an invitation from the Royal Institution to become one of its lecturers.