In 1977 he became Vice President of the Florida Baptist Convention, and was then its President from 1981-1994. In 1994, Lyons became President of the National Baptist Convention USA Inc.

In 1999 Lyons was sentenced to a total of five and a half years in jail for misappropriating more than $4 million from the NBC while he was its President.

In April 2007 Lyons was defeated in an attempt to be re-elected President of the Florida Baptist Convention. Subsequently he and his supporters organized the General Baptist State Convention of Florida, of which he is the President. He will run for National Baptist Convention Presidency in 2009.