In the first year of the new century, William Allen's father died, and the family silk business was thereafter managed by his father's assistant. This left William free to grow his own business in the field of pharmacy, gradually becoming independent and establishing his own business. 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.
In 1807, Allen's original research (on carbon) enabled him to be successfully proposed for election to Fellowship of the Royal Society, bringing him into contact with those who were publishing much of the original scientific research of the day. This strengthened his ties with the eminent Humphry Davy, and in due course with his longstanding friend Luke Howard who was likewise elected to Fellowship of the Royal Society, though some years later.
In 1841 William Allen co-founded the The Pharmaceutical Society, which later became The Royal Pharamaceutical Society. Its first president was William Allen.
Allen's involvement with the Plough Court Pharmacy began in the 1790s when he began working there for Samuel Mildred. Already a thriving business in the City of London, with the arms of the Apothecaries Company emblazoned on its window, it continued to prosper and William Allen was offered a partnership; the company thereafter trading for a while under the name Mildred and Allen. William Allen strengthened the company's links with medical institutions, particularly Guy's Hospital where he was elected to its 'Physical Society'. Meanwhile, using the facilities at Plough Court for meetings, he was able to broaden such associations further by co-founding the Askesian Society through which new ideas for research and experimentation could be discussed with others such as Luke Howard, Joseph Fox, W.H.Pepys, Dr Babington, and the eminent surgeon Sir Astley Cooper. In 1797 William Allen invited Luke Howard to formally collaborate with him at the Plough Court Pharmacy, the business becoming known as Allen and Howard to reflect this partnership. As the business expanded, a second laboratory was opened for the development of new chemicals, a few miles from the company's City of London headquarters, in Plaistow.
His self sufficient settlement was described in detail in his pamphlet "Colonies at Home", where he stated "instead of encouraging emigration at enormous expense per head let the money be applied to the establishment of Colonies at Home and the increase of our national strength". To the people of the time (1820s) the known colonies were in the Americas so the whole area became known as "America". This identity remains in the local street names and people's memories of the cottages in what is now America Lane.
William Allen's other philanthopic interest was education. He became greatly influenced by the ideas of Joseph Lancaster. In 1810 William Allen became treasurer of the Royal Lancastrian Society, whose aim was to open progressive schools in England and abroad. It was renamed the British and Foreign School Society in 1814, when Allen was again its treasurer. From 1824 to 1838 William Allen ran a novel Quaker school for girls at Fleetwood House and in its park-like grounds at Stoke Newington, now part of Abney Park Cemetery. Here he was able to ensure the girls were taught the new sciences as well as conventional subjects. The school also introduced the first school bus in the world, a Shillibeer.
In 1811 William Allen, with the support of James Mill, started a publication entitled the Philanthropist. It published articles by Mill and by Jeremy Bentham. In 1816 he became a founding member of the Peace Society, a political development from his longstanding Quaker pacificism. From 1818-1820 he toured Europe with the Quaker evangelist Stephen Grellet.
The society had always been strongly influenced by the Friends, and particularly by London-based Quakers. All the members of its predecessor committee (1783-7) had been Quakers, and nine of the twelve founders of the subsequent non-denominational 'Society for the Abolition of the Slave Trade' were Quakers, including two - Samuel Hoare Jr and Joseph Woods Sr (father of the botanist Joseph Woods Jr) - who lived close to William Allen in Stoke Newington, the village near London where Allen had family interests after his second marriage in 1806.
Perhaps the best known committee member of the new non-denominational abolition society, founded in 1787, was William Wilberforce, who, unlike its Quaker members, was eligible as an Anglican to be elected to, and sit in, the House of Commons. Wilberforce visited William Allen at his experimental gardens in Stoke Newington on several occasions in his role as the Society's parliamentary representative. He had long been familiar with the village, owing to residence there of his brother-in-law James Stephens' father at Summerhouse - a large house adjoining Abney Park in the very grounds of the mansion that later, in the 1820s, was to become William Allen's novel girls' school.
William Allen was also a founder member and a Director of the African Institution; the successor body to the Sierra Leone Company, sponsored by philanthropists to establish a colony in West Africa for slaves freed on a voluntary basis, through the abolitionists' efforts, in America. The work of the successor body began in 1808, when the colony had been handed to the Crown in return for the British Parliament passing legislation for its protection at about the same time as the passing in 1807 of the Act for the abolition of the slave trade.
William Allen's active interest in the abolitionist cause continued until his death. In the mid 1830s he was passionate about abolition of the apprenticeship clause, and achieving the complete freedom of African-Caribbean people on 1 August 1838. His biographer James Sherman records, 'the apprenticeship clause in the Bill... had been greatly abused by the planters. Mr Allen was indefatigable in his efforts, by interviews with Ministers and official persons.. His account of the spirit-stirring time is graphic:',
In 1839 William Allen became a founding Committee Member of the British and Foreign Anti-slavery Society for the Abolition of Slavery and the Slave-trade Throughout the World, which is today known as Anti-Slavery International. In this role he was an organiser of, and delegate to, the world's first Anti-slavery convention, which was held in London in 1840 - an event depicted in a large painting by Benjamin Haydon that hangs in the National Portrait Gallery, London.
In 1806 William Allen married for the second time. His new wife, Charlotte Hanbury of Stoke Newington was the daughter of a similarly affluent Quaker family. The marriage led to a longstanding association between William Allen and Stoke Newington. The couple visited the continent in 1816, but Charlotte died during their travels, leaving him to bring up his daughter Mary. Tragedy struck again in 1823, when Allen's daughter Mary (recently married to Cornelius Hanbury) gave birth to a son but died just nine days later.
William Allen married for the third time in 1827. This marriage was the subject of public comment, since his betrothed - Grizell Birbeck (formerly Grizell Hoare of Stoke Newington) - was an elderly Quaker widow. A satirical cartoon was published by Robert Cruikshank (brother of the more famous George) depicting Allen and his elderly fiancee in 'Newington Nunnery' the novel Quaker girls' school of which he was so proud. This marriage was as tragic as his first two, for Allen's wife Grizell died in 1835, leaving him single for a third time. However, he had a large circle of friends, and was able to afford to travel extensively. In 1840, for example, he travelled for five months across Europe with Elizabeth Fry and Samuel Gurney.