Upon retiring, Guerra becomes head coach of Atlético Potosí, starting off with the youth reserves and eventually going to lead the first team in the 1979-1980 season. After San Luis, Guerra coached Club Deportivo Guadalajara twice, with whom he crowned in the 1986-1987 season and two runners-up runs in 1982-1983 and 1983-1984. In 1990, Guerra won the Copa México with Leones Negros de la U. de G. defeating Club América, in the same season he reaches the final, but loses against the Puebla F.C. of Manuel Lapuente, with an aggregate score of 6-3. After winning back to back championships in the Primera "A" with Tigres de la UANL during the Torneo Invierno 96 and Verano 97, Guerra reaches promotion to the Primera División de México for the tournament of Invierno '98.