After Puel's departure and the appointment of new manager Didier Deschamps, Squillaci joined Monaco in 2002. In his first full season as a player for his side, facing Real Madrid in the quarter-finals of the 2003–04 UEFA Champions League, Monaco progressed despite losing 4–2 in Madrid, due to the 3–1 victory in the return leg; the side advanced through to the semi-finals on the away goals rule, where they defeated Chelsea. Their run came to an end when they suffered a 3–0 defeat to FC Porto in the final. Squillaci made 217 appearances for the club over six seasons.