In 1913 he returned to Wales to be near to his elderly father. Joining the civil service, he was appointed chief inspector of the Welsh office of the Board of Agriculture. For twenty-five years in this role, he developed agricultural education, and founded Wales' four agricultural institutions. He was presented with a M.A. degree in 1918 from his college in Oxford, and was given an M.Sc. the same year.
In 1937, aged 60, he resigned from the Ministry of Agriculture and accepted a job as the Principal of the Presbyterian College, Carmarthen. Despite his lack of religious zeal, Jones was well received at the college and made efforts to reform and expand the institution.
Watcyn and his wife retired to Llandre near Aberystwyth, and he died aged 87 on October 17, 1964.[2]