Mavrogenidis is best known as Olympiacos' first-choice right-back for a long stretch of the club's dominance of Greek football in the late 1990s and early 2000s.
Upon arriving from Aris, Mavrogenidis established himself as Olympiacos' first-choice right-back for the next nine seasons, during which time Olympiakos dominated Greek football.
Mavrogenidis also made two European appearances with Iraklis—the Thessaloniki club qualified for the 2006–07 UEFA Cup, but was eliminated in the first round of the competition by Wisła Kraków, 2–1 on aggregate after extra time.
[17] After leaving Iraklis in 2008, Mavrogenidis signed with newly promoted Greek Super League side Thrasyvoulos.
Mavrogenidis made 21 appearances (17 starts) for Thrasyvoulos in 2008–09, but at the end of the season the team was relegated back to Beta Ethniki.