In 2019, after a period at Chapecoense, Batista became an under-15 coach at América Mineiro. On 13 October 2020, he was named in charge of the club's under-20 squad.[3]
William left América on 14 November 2022,[4] and was named head coach of Vasco da Gama's under-20 team eight days later.[5] On 23 June of the following year, he was named interim head coach of the main squad, after Maurício Barbieri was sacked.[6]
Batista was in charge of Vasco for three matches, becoming the club's youngest head coach in the century,[7] before returning to his previous duties after the appointment of Ramón Díaz. He was also in charge of the first two matches of the 2024 Campeonato Carioca, as the first team was away on pre-season, but was sacked on 22 January of that year.[8]
On 26 February 2024, Batista was appointed head coach of the under-20 team of Red Bull Bragantino.[9] He left the side in August to return to América, as an assistant of Lisca.[10]
On 6 December 2024, Batista was named head coach of América for the upcoming season.[11]