Barcena has deployed more than 100 policemen at the Climaco Freedom Park, also known as Abong-Abong Park, where thousands of devotees flocked for the station of the cross.
Barcena's personnel were backed by troops from the military's Task Force Zamboanga (TFZ).
"So far (it was) peaceful," Barcena said through a text message Saturday.
The police also guarded the "Santo Intiero" procession held downtown in the afternoon of Good Friday.
Aside from the Immaculate Metropolitan Cathedral, similar processions were also held in some of the parishes in Zamboanga City.
In the downtown and other parts of the city, traffic flow was smooth despite several streets which were closed to give way for the procession.