Porthmadog and Connah's Quay joined the newly formed Cymru Alliance, Bethesda remained in the Welsh Alliance League. Return to Caernarfon & District/ Gywnedd Leagues After finishing third in the Welsh Alliance in 1990–91, the club decided to drop down to the local Caernarfon & District League where they remained until stepping up to the Gwynedd League after being crowned champions in 1997–98 season. After two seasons in this league they were promoted to the Welsh Alliance League in 2000 after being crowned champions for the 1999–2000 season. Welsh Alliance success The club spent nine years in the Welsh Alliance culminating in two successive championship winning years. In the 2007–08 season they were champions of the Welsh Alliance League but were refused promotion to the Cymru Alliance by the Football Association of Wales. Two players, Gareth Davies and Richie Owen, scored 70 goals between them over the course of the season. The following season saw the club break the league's season goal-scoring record, with 146 goals - again securing the league title. After also completing upgrades to their football ground, the club stepped up to the second tier of Welsh football – the Cymru Alliance. Cymru Alliance The club spent a solitary season in the Cymru Alliance, finishing 9th from 17 clubs in 2009–10 season. Return to the Welsh Alliance The club returned to the Alliance, competing for two subsequent seasons. In August 2012 they were not able to complete fixtures and were given 14 days by the league's Management Committee to resolve their issues. The club announced in September that it was disbanding and resigned from the league "due to various circumstances". After a season away - the club returned for the 2013–14 season but finished bottom of the Welsh Alliance Division 2 with just 6 points. The following season saw them finish 10th from 16 clubs, before they again left the league. Return to the Gwynedd League The club returned to the Gwynedd League, finishing bottom of the league in the 2016–17 season. The following season they withdrew from the league. In 2018 it was announced that the club would return to the league again but they again resigned from the league in August 2018 without playing any games. They were named as a returning club for the 2019–20 season to same league. Ladies The club also has a ladies team, Bethesda Athletic Ladies, who were established in 2018.