He was an early supporter of the Cymru Fydd movement, but opposed its integration with the South Wales Liberal Federation, thus making an enemy of David Lloyd George, being largely responsible for that movement's demise. As President of the South Wales Liberal Federation from 1894–97, Thomas believed that the southern counties of Glamorgan and Monmouthshire, which together contained over half the Welsh population, would suffer under the proposed scheme for a single national federation. He held similar views on the disestablishment of the Church in Wales, believing that the revenues wrested from the church should be distributed to the counties on the basis of population. With David Lloyd George, Francis Edwards and Herbert Lewis, Thomas revolted against the Rosebery Government's perceived downgrading of Disestablishment in 1894.