Peeters replaces Jose Riga, who guided the Addicks to Sky Bet Championship safety but then left the club at the end of his short-term contract.
The 40-year-old retired from the playing ranks in 2008 and this will be his fourth coaching role after spells with Cercle Brugge, Gent and most recently Waasland-Beveren.
Peeters has experience of south London, having spent parts of three seasons with Millwall.
He will work alongside Damien Matthew, Charlton's former Academy manager and current first-team coach.
However, former assistant manager Alex Dyer has left the club after three-and-a-half years at The Valley.