Machlas was born June 16, 1973 in Heraklion, Crete. He started his football career with local club OFI FC in 1991. Following the 1996 season, he moved on to Vitesse Arnhem and the Dutch League, the so-called Eredivisie.
Following the 1998-99 season Vitesse president Karel Aalbers wanted to sell Machlas to a foreign top club but Machlas really wanted to go to Ajax. "Ajax is for me the perfect team", said Machlas in an interview to soccer magazine Sportweek. The European topscorer signed a new contract with Ajax beginning of July 1999. The transfer sum was about US$ 12 million. He was the first Greek to ever play for Ajax. Machlas had chosen Ajax while other top clubs like Fiorentina and Arsenal, expressed interest in signing him.
He retired after the 2008 Cyprus Cup final (May 17, 2008), APOEL - Anorthosis 2-0. In an interview Machlas said: "This was the last game of my career. It has come to a completion, exactly as I wanted it to be. With a title!"
His career ended having played a total of 462 games and 196 goals scored.