In December 2008, the duo was appointed in River Plate.[3] In 2011, he was once again appointed as assistant manager of River Plate, this time under manager Matías Almeyda.[4] A half year later, he was appointed as the manager of Independiente Rivadavia.[5] He was fired on 25 February 2019, after the team conceded 10 goals in two games.[6]
In November 2012, Zapata took over the reserve team of River Plate.[7] From May 27 to May 30, Zapata was the caretaker manager of River Plate following the departure of Ramon Diaz.[8] On 11 February 2015, Zapata and his staff was surprisingly fired.[9]
In the summer 2015, Zapata was then appointed as the manager of Racing Club's reserve team.[10]
In December 2015, Néstor Gorosito was appointed as manager of Spanish club UD Almería and took Zapata with him as his assistant.[11] On 12 February 2019, Zapata was appointed as the assistant manager of Néstor Gorosito at Tigre.[12]
