He was born in Amsterdam and worked as an engineer in a machine factory at Rotterdam and on a Rhine barge before he contacted the DZV (Doopsgezinde Zendings Vereeniging) in 1851 with a request to be sent as a missionary.
[1][2] Klinkert was educated as a surveyor, and received training in the seminary of the Nederlandsche Zendeling Genootschap (NZG) at Rotterdam for his future missionary service.
Klinkert was an older student and it was therefore more difficult for him to accept guidance but S. Hoekstra who was the pastor of the Rotterdam Mennonite church would defend him.
Shortly after she died in 1870, Klinkert married Willemina Samuela Diderika Roering (1844–1929) who brought a child of her own into the union.
They also visited nearby villages together on horseback where Klinkert started to lead house services in the Malay language.
His profession was a lecturer and he worked at the Institute, which merged with the University of Leiden in 1890, until 1904, teaching Malay and literature to first and second year students.
In the Old Testament Klinkert used Allah as a translation for the singular Hebrew Elohim, and used ilah, as well as dewa, and berhala for plural gods.