Alonso arrives from Atletico Madrid, where he spent nine years inside their youth system. Last season he coached the club's U15 team.
Alonso said of his appointment: “I’m really happy to be joining the Crystal Palace Academy.
“My goal is to play good football, compete in every game, and to improve the team. I want the players to establish a winning mentality; if we play well, we will have a greater chance of progressing.
“We have a good squad and want to be competitive in the league, so I am looking forward to this season.”
Academy Director Gary Issott added: “The club went to great lengths to identify the right candidate through a thorough recruitment process and Javier was the outstanding candidate from the outset. We’re delighted to have him on board.”