Bacterial pathogens use specialised secretion systems to colonise their hosts and cause disease. Secretion systems inject toxins into the host cell to aid bacterial pathogenesis and inhibit host immunity. Many secreted bacterial toxins modify host proteins during infection but their potential to target host RNA is currently unknown. In this study, we developed dual RNA-interactome capture (Dual-RIC) to isolate bacterial toxins that interacted directly with host messenger RNA (mRNA) during Legionella pneumophila infection. Dual-RIC identified several Legionella toxins associated with host mRNA, including a novel toxin important for bacterial pathogenesis in vitro and in vivo. This toxin localised to the host nucleus via interactions with components of the nuclear envelope and preferentially bound to guanine-rich motifs within its mRNA substrates. Using structural and biochemical approaches, we then isolated the RNA-binding site within this toxin which overlapped a NADPH-binding site required for its oxidase activity. Our findings suggest that RNA-targeting may be an important regulatory mechanism for NADPH oxidases that limits oxidative stress and inflammatory responses to infection.