The Brazilian defender flew out to Turkey to complete the move after the two clubs worked out a deal.
Lyanco was expected to complete the transfer as Southampton continue to cut down their squad following relegation from the Premier League.
But the centre-back’s proposed move to Besiktas has fallen through after they noticed a problem with his medical.
According to Turkish broadcaster A Spor, the Turkish giants saw a problem in his knee cartilage, which forced them to pause the move.
Besiktas carried out more checks and even did another test on his knee and were left unsatisfied.
The club backed out of the deal as they did not want to sign a player who is carrying a knee injury.
Lyanco will now return to pre-season training with Southampton as his agents look to find him a new club.
It remains to be seen whether the defender undergoes a rehabilitation process to fix his knee before seeking a transfer.
