The Portuguese leaves his job as U21 coach at Chelsea after just one year to become No2 to manager Liam Rosenior at Strasbourg.
Academy technical director Glenn van der Kraan told Chelsea's website: "Despite his time with us lasting just over a year, Filipe has made an important impact on our programme, influencing our football identity, enforcing the highest of standards and performing at the highest level every single day.
"This is a fantastic opportunity for Filipe to continue his coaching journey and we look forward to seeing where that takes him in the future."
Calum McFarlane will step into the role of Under-21s head coach following his recent arrival from Southampton, supported by former Chelsea Academy players Andy Ross and James Simmonds.