Appointed in 1892, the year of their admission to the Football League, he oversaw the club winning the inaugural Football League Second Division championship, promotion to the First Division the following year, and two further promotions before his retirement in 1908.
That season they reached the semi-final of the FA Cup, which brought money into the club and broadened popular awareness of it.
It was at this point that Jones became the club's first paid secretary, and in addition took over responsibility for team affairs.
In Jones's first season as secretary-manager, Small Heath won the inaugural Second Division championship, though this did not bring automatic promotion; the club were unsuccessful in a test match against the bottom club in the First Division, Newton Heath.
After the 1908 relegation, Jones was replaced as secretary-manager by Alex Watson, though he stayed at the club as part-time accountant until the First World War.