The civil war that occurred in El Salvador during the 1980s affected Juventud Independiente, as players fled the country and the sheer danger of watching the games kept fans away.

In 1989 just before a promotion play-off against San Rafael Cedros, a major offensive was launched and many players fled the country causing Juventud Independiente to lose the match.

During the nineties, the team expanded and reached second division for the first time in several years after defeating Juventud Olímpica 5–1 on aggregate.

Ramon Sanchez worked hard with the young players of Juventud Independiente and eventually reached the play-off.

The team won on their second attempt and were promoted to second division, beginning the emergence of young stars Henry López and Carlos Asprilla.

After securing a spot in the second division, they were able to sign foreign players such as Rodrigo Lagos, Fainor Viáfara and Carlos Escalante.

However, this changed in the 2013 Clausura when the club were able to qualify to the semi-finals as the fourth placed team after winning a dramatic play-off with Santa Tecla 1–0.

This was largely due to the new addition of Nigerian Agustin Jibirin, David Antonio Rugamas, top goalscorer for the season Uruguayan Jesus Toscanini, and Jose Luis Gonzales.