Mercer continued to work at Oakenshaw for the rest of his working life. He was made partner in 1825, in which role he remained until 1848. 

He was a great innovator, not only creating colours and colour mixes that were the height of fashion, but also devising new processes of dyeing and other related matters. He also was interested in medicine and developed an 'iron' medicine. 

The local soap works at Enfield asked for his help, and he developed a method of bleaching palm oil. He developed red ink. He was always ready and willing to give considerable thought to technical problems.

He gained tremendous support from other chemists in the area, and was soon befriended by the young Lyon Playfair when he came to work at Thomson's Primrose Works in Clitheroe. 

It was Playfair who encouraged him to agree to be elected as one of the original Fellows of the Chemical Society in 1842.