After retiring, César Sampaio worked as a
director of football of
Pelotas,
Rio Claro and
Mogi Mirim. On 4 November 2011, he returned to Palmeiras under the same role, departing on 21 January 2013, after the club's relegation. César Sampaio was named the director of football of
Fortaleza on 23 November 2016, but left his role on 3 March of the following year. In January 2015, he became the president of
Comercial do Tietê. On 22 December 2019, César Sampaio left Comercial to join
Tite's staff at the Brazil national team, as his assistant. He was a part of the coaching staff during the
2022 FIFA World Cup, leaving with Tite in late 2022. In October 2023, César Sampaio moved to
Flamengo, again as Tite's assistant; the duo left nearly one month later. On 4 January 2025, he returned to his first club Santos, as permanent assistant coach. On 14 April 2025, César Sampaio was named interim head coach of
Peixe, after
Pedro Caixinha was sacked. On his coaching debut two days later, his side defeated
Atlético Mineiro 2–0 at home. Back to his assistant role after the appointment of
Cleber Xavier, César Sampaio became a technical coordinator at Santos on 22 August 2025. ==Career statistics==