The club stayed on the top spots of the national tournament during most of the 2000s and gained qualification to the Copa Libertadores eight years in a row from 2000 to 2007. It would only win two titles during the decade which were obtain in 2002 and 2005 with many notable players as Sergio Leal, Jorge Soto and Luis Alberto Bonnet. However, during the 2007, Cristal would come four points away from relegation. It would make a comeback during the 2008 season and qualify to the Copa Libertadores once again.