Context. Variability has proven to be a powerful tool to detect active galactic nuclei (AGN) in multi-epoch surveys. The new-generation facilities expected to become operational in the next few years will mark a new era in time-domain astronomy and their wide-field multi-epoch campaigns will favor extensive variability studies. Aims. We present our analysis of AGN variability in the second half of the VST survey of the Wide Chandra Deep Field South, performed in the r band and covering a 2 sq. deg area. The analysis complements a previous work, in which the first half of the area was investigated. We provide a reliable catalog of variable AGN candidates, which will be critical targets in future variability studies. Methods. We selected a sample of optically variable sources and made use of infrared data from the Spitzer mission to validate their nature by means of color-based diagnostics. Results. We obtain a sample of 782 AGN candidates among which 12 are classified as supernovae, 54 as stars, and 232 as AGN. We estimate a contamination ≲20% and a completeness ∼38% with respect to mid-infrared selected samples.