The next year, he started the Barcelona Foundation, to prevent the conversion of the club to a private-owned sporting society, per the new Spanish law.

Months later, he survived a vote of no-confidence instigated by opponent platform "L'Elefant Blau", one of whose leaders, Joan Laporta, would become the club's president several years later.

His refusal to pay high wages gained him many critics and saw the departure of players like Diego Maradona, Ronaldo, Bernd Schuster, Hristo Stoichkov and Luís Figo.

On 28 July 2011, Nuñez was sentenced to six years in prison, like his son José Luis Núñez Navarro, and to pay a fine of two million euros for the crime of bribery – and another 36,000 euros fine for documentary falsification due to his involvement in the "Hacienda Case", offenses of which he has always declared himself innocent.

He was also sentenced financial adviser of the Núñez, Salvador Sánchez Guiu, to six years of prison and 2 million euros of fine.

Subsequently, the Tax Agency made new verification and investigation actions on the exercises included in the process and concluded that there was no type of fraud.