The bishop went to Kinsale, inquiring into the rumours which preceded the Spanish Armada, and for years afterwards he kept an eye on those who were in correspondence with Spain.
Lord Deputy William FitzWilliam, who did not have an especially high opinion of Church of Ireland bishops, wrote enthusiastically to Walsingham about Lyon's early evangelism: in 1589 and 1590 he had sometimes congregations in the thousands.
He took a moderate line that the Irish would respond to justice, and the soldiery was harmful to his cause, but wanted the exclusion of priests from abroad.
When Sir Thomas Crooke, founder of Baltimore, was accused of piracy in 1608, Lyon was among his strongest defenders, arguing that he had worked miracles in creating a thriving town out of nothing in barely three years.
Lyon, who lived to a good age, died at Cork on 4 October 1617, and was buried in a tomb which he had raised for himself twenty years before in the palace grounds.
This was probably not Mary, who apparently died in 1617, having married Henry Becher, who for a time was acting Lord President of Munster: their grandson was the politician Thomas Beecher.