Samuel Jones was neither ordained nor instituted by a bishop, but admitted to the living of Llangynwyd on the authority of Oliver Cromwell who was trying to increase the quality of vicars. Anglicans would have held that he was an 'intruded' minister and that his appointment was unlawful. This scholarly man, having been converted to puritanism while at Oxford, abandoned a promising academic career to become a minister of the gospel at Llangynwyd. His congregation were not very supportive, but he was supported by a small but ardent group of Puritans. With the return of Charles II in 1660 Jones remained in his living for two years, but gave it up when he refused to sign the Act of Uniformity which tried to re-establish Anglo-Catholicism. He joined 2,000 other good men out of a job. He settled at Brynllywarch and remained there for the rest of his life.
For 35 years Jones carried on his work in the puritan cause. He ministered to small congregations of committed dissenters in the area (although this would have been dangerous up to the Toleration Act of 1689). He is best remembered for his teaching work in this house. Here the former Oxford scholar tutored sons of the gentry and young men preparing for the dissenting ministry. His fine qualities as an educator were recognised by the award of grants from the Presbyterian and Congregationalist funds; several students became noteworthy ministers.
After his death in 1697, the work of the Brynllywarch Academy, as it became known, was transferred to different places in turn, and the name of Samuel Jones went into eclipse.