Greenwich won a third League Cup in 1997–98. After five consecutive top-half finishes between 2006–07 and 2010–10, Greenwich finished bottom of the Kent League in 2011–12. The league was renamed the Southern Counties East League in 2013, and in 2014–15 the club won the Premier Division Cup. The following season saw them win the league, earning promotion to Division One South of the Isthmian League. In 2016–17 the club finished third in the division, qualifying for the promotion playoffs. However, they lost 4–3 to Corinthian-Casuals in the semi-finals. Although a fourth-place finish the following season saw the club finish fifth and reach the play-offs again, they lost 3–0 to Corinthian-Casuals in the semi-finals. At the end of the season they were moved into the South East Division as the league was reorganised.