Morgan was ordained in 1884, and took charge of the Congregational mission at Llanwddyn, where he ministered to the villagers and the workmen engaged in the construction of the Liverpool Waterworks at Lake Vyrnwy.
In London, Morgan became known as a hard-working, enthusiastic minister, his wife, Sarah, filling his pulpit on a number of occasions.
Thomas Edward Ellis also spoke at the chapel, and it was rumoured that Vyrnwy Morgan was planning to enter parliament.
In 1899, Vyrnwy Morgan left Nebraska, on account of his wife's poor health, which he attributed to the climate, relocating to Denver.
In 1908, Morgan left Cardiff, spending some time at the family home in Cwmafan, following the death of his father, before moving to West Wales, initially settling at Aberystwyth.
It was in 1909 that Vyrnwy Morgan finally broke with Nonconformity, being received into the Church of England, Although he occasionally spoke under special bishop's licence, he was not re-ordained, although he continued to style himself 'Reverend'.
The same year, Morgan married Margaret Greig of Edinburgh, by whom he had one child, a daughter, Jean (born November 1910).
At the 1910 General Elections, Vyrnwy Morgan was a visible and vocal Conservative supporter, addressing audiences in England and Wales.