The influence of residual cuts on the deactivation of hierarchical Y zeolite-based catalysts during the co-processing of vacuum gas oil (VGO) with atmospheric residue (ATR) was investigated. The experiments were conducted in a laboratory-scale MAT-type reactor. The conversion of VGO, ATR, and their 70:30 (mass basis) mixture was examined using two composite catalysts: Cat.Y.0.00 and Cat.Y.0.20. The operating conditions closely resembled those of the commercial catalytic cracking process (550 °C and contact times of 10 to 50 s). When ATR was processed individually, the conversion remained below 50 wt%. However, significant improvements in conversion rates were achieved and catalyst deactivation was mitigated when ATR was co-processed with VGO. Notably, the BET surface area and average mesopore volume were adversely impacted by ATR, which also led to the accumulation of high levels of metals and nitrogen on the spent catalyst, detrimentally affecting its acidic and structural properties. Moreover, substantial coke deposition occurred during ATR cracking. The soluble and insoluble coke analysis revealed H/C ratio values of up to 0.36, indicative of polycondensed coke structures with more than ten aromatic rings. The nature of the coke was confirmed through TPO and FTIR analyses. Interestingly, the CatY.0.20 catalyst exhibited less activity loss, retaining superior acid and structural properties. Co-processing Colombian atmospheric residue with ATR loadings of 30 wt% (higher than the typical 20 wt%) in catalysts formulated with hierarchical zeolites presents a promising alternative for commercial applications. This research opens avenues for optimizing catalytic cracking processes.