Metacaspases (MCs) are cysteine proteases that are implicated in programmed cell death of plants. AtMC9 (Arabidopsis thaliana Metacaspase9) is a member of the Arabidopsis MC family that controls the rapid autolysis of the xylem vessel elements, but its downstream targets in the xylem remain uncharacterized. PttMC13 and PttMC14 were identified as AtMC9 homologs of hybrid aspen (Populus tremula x tremuloides). A proteomic analysis was conducted in xylem tissues of transgenic hybrid aspen trees which carried either an overexpression or an RNAi construct for PttMC13 and PttMC14. The proteomic analysis revealed modulation of levels of both previously known targets of metacaspases, such as Tudor staphylococcal nuclease, heat shock proteins and 14-3-3 proteins as well as novel targets, such as homologs of the PUTATIVE ASPARTIC PROTEASE 3 (PASPA3) (PASPA) and the cysteine protease RD21 by PttMC13 and PttMC14. We identified here the pathways and processes that are modulated by PttMC13 and PttMC14 in xylem tissues. In particular, the results indicate involvement of PttMC13 and/or PttMC14 in controlling not only xylem cell autolysis but also cell death. This work provides a valuable reference dataset on xylem specific metacaspase functions for future functional and biochemical analyses.