He worked as estate manager to Sir Thomas Bilson, of West Mapledurham House (demolished 1829), near Buriton, and also as agent for two Bishops of Winchester: Thomas Bilson (father of Sir Thomas Bilson) and later, Lancelot Andrewes. Goodyer developed a great interest in botany, and added many plants to the British flora. He is credited with clarifying the identities of the British elms, and for discovering an unusual elm endemic to the Hampshire coast between Lymington and Christchurch named for him as Goodyer"s Elm.
This was believed by the botanist Ronald Melville to be a form of the Cornish Elm.
Goodyer gained the reputation of being "the ablest Herbalist now living in England". He is also believed to have introduced the Jerusalem Artichoke to English cuisine, but perhaps his most enduring legacy was his revision, with Thomas Johnson, of Gerard"s Herbal, the greatest herbal of its time.
He also translated a Latin version of Dioscorides"s work, "De Materia Medica". Goodyer lies in an unmarked grave near his wife"s at Street Mary's church, Buriton, where a stained glass window can be found as a memorial to him, showing the Goodyer coat of arms.
Indeed, Goodyer"s reputation was such that in 1643 during the English Civil War, Ralph Hopton, one of the senior Royalist commanders, ordered troops "to defend and protect John Goodyer, his house, family, servants and estates".