Caersws survived relegation for a second straight year after ENTO Aberaman Athletic failed in their appeal to get a domestic licence after their floodlights were not up to the Welsh FA's expectations.
In a good first leg for both sides, Llanelli produced the shock of the round with a 1–0 away win against Motherwell, giving them a wonderful chance of progression.
Bangor City were the only Welsh side in European competition when they started their Europa League campaign in the second qualifying round against FC Honka from Finland.
They had hope of progression and this was compounded by a positive 2–0 defeat in Finland, but they lost the home leg 1–0, which knocked them out and ended Wales' participation in European competition for 2009.
The Welsh league picked a disappointing 0.250 for their participation in European competition in 2009, the only points coming from Llanelli's away win against Motherwell.