Early career Beqaj began his profession career in
Kosovo with local side
Liria Prizren in 1992. He then moved to
Tirana, Albania at the start of 1995 to attend university, where he was to play for
Partizani Tirana. He played in Albania for two and a half years as he left in 1997 to join
OFI after being spotted playing for
Albania U-21s.
Greece He spent six seasons at OFI, where he played 129 league games for the Greek side and even scoring a goal in the 2000–01 season. Beqaj then signed for
Ionikos where he made 83 league appearances in three seasons before ending his nine-year stint in Greece.
Anorthosis Famagusta Beqaj was one of the most important players that helped
Anorthosis Famagusta reach the group stages of the
UEFA Champions League for the first time in history in the
2008–09 season. The team started their campaign in the
first qualifying round where they faced
Armenia's
Pyunik. It was an easy task for Anorthosis who won both matches with Beqaj keeping two clean sheets. In the
next round against
Rapid Wien, Beqaj kept a clean-sheet in the first leg but was beaten three times in the second leg but nevertheless Anorthosis progressed 4–3 on aggregate. Beqaj was named
man of the match in the second leg of
third qualifying round against
Olympiacos, making several vital saves in a 1–0 narrow loss which was enough to clinch to qualification to group stage after a 3–0 win in the first leg. By doing so, Anorthosis made history by becoming the first
Cypriot team to ever qualify for the Champions League group stages. ==International career==