On 12 March 2021, Núñez, along with 10 other former ministers as well as former president Jeanine Áñez were charged with terrorism, sedition, and conspiracy in relation to what the new government described as the coup d'état which brought Áñez and her ministers to power in the 2019 political crisis. Núñez denounced the actions as a "witch hunt" and pointed out that the alleged coup "refers to events that occurred before the Áñez government assumed command of the country." That same day, Núñez's nephew Gary Tudela reported that 20 policemen had raided the house of the former minister's mother without showing either an arrest warrant nor a search warrant. On 18 March, Núñez's son Antonio Núñez was held in police custody in order to collect "data" about his father. He was released hours later and took refuge at the Beni Civic Committee.