In 1991, the second year after returning to the Chilean First Division, still having Manuel Pellegrini as coach, was not very good, as he finished in 9th place in the league, but reached a significant semifinal of the Chile Cup, in Which only was defeated by Universidad Católica on penalties (4-3), after having tied 1-1 in the both former matches.

Then the club has some hard years, where until 1998 did not rise from the 10th place on those tournament, struggling places of the bottom of the table of positions.

Within the poor results, in 1994 the equipment suffers the worst beating of its history (1-10) made by Universidad Catolica.

Even in 1996 he went to the relegation playoffs (where it had to play against a second division team for keeping the categoy), in which he lost 1-0 against Deportes Iquique visiting, and local won 5-1, maintaining the category.

Anyway, Palestino had players who stood out, among them: Anibal ‘Tunga’ Gonzalez (first division scorer in 1995), Marcelo Corrales and Jaime Valdés (who was finally transferred to Italian football).

In 1999, with Ricardo Dabrowski, the team had a good job, qualifying for the final round of the tournament (in 7th place), and finishing in the 6th position. Also in this tournament is counted the match with the best thrashing that has had Club Deportivo Palestino: 9-0 to Deportes Temuco.