We assessed the off-target effects of M2 expression on the leaf proteome of Nicotiana benthamiana infiltrated with the bacterial gene vector Agrobacterium tumefaciens. A iTRAQ quantitative proteomics procedure was followed to compare the leaf proteomes of plants agroinfiltrated with either an ‘empty’ vector or an M2-encoding vector. Leaves infiltrated with the empty vector had a low soluble protein content compared to non-infiltrated control leaves, associated with increased levels of stress-related proteins but decreased levels of photosynthesis-associated proteins. M2 expression partly compromised these effects of agroinfiltration to restore soluble protein content in leaf tissue, associated with restored levels of photosynthesis-associated proteins and reduced levels of stress-related proteins in the apoplast. These data illustrate the cell-wide influence of Golgi lumen pH homeostasis on the leaf proteome of N. benthamiana responding to microbial challenge.