On his return to Glasgow in 1882 Henry Dyer lived in Lenzie, near Glasgow, for a few years. Thereafter, from about 1885 until his death in 1918,he lived, with his wife Marie and family, at 8 Highburgh Terrace (now 52 Highburgh Road) in the West End of Glasgow, not far from the University of Glasgow. Although he was not successful in obtaining an appointment to a senior University post on his return, he became involved in a wide range of educational activities at university and school levels in the West of Scotland. His engineering work was recognised by the University of Glasgow in the award of the DSc degree in 1890. He was also honoured by Glasgow University through the award of an honorary LLD in 1910. In 1914 he became a JP. He pursued many interests in other activities, mainly of a cultural and religious nature while maintaining a strong interest in all things to do with Japan throughout the rest of his life.

Henry Dyer died on 25 September 1918. His gravestone is in the Necropolis cemetery in Glasgow.