In this study, a systematic review and meta-analysis were conducted to summarise available information on the occurrence of Salmonella spp. Listeria monocytogenes and shigatoxin-producing Escherichia coli (STEC) in fruits and vegetables sold at retail establishments in several European countries. Overall, L. monocytogenes was the main pathogen detected in all kinds of vegetables, packaged or not (3.4%; 95% CI: 2.1–5.4%) with Salmonella spp. being the pathogen of lowest incidence (0.9%; 95% CI: 0.5–1.2%). The pooled occurrence rate of pathogens in either packed or unpacked vegetables was estimated at 1.9% (95% CI: 1.2–3.1%), with 2.1% of prevalence (95% CI: 1.3–3.4%) for unpacked vegetables and 1.7% (95% CI: 0.9–2.9%) for packed ones. For the three pathogens, the category of spices and herbs was the most frequently contaminated with pathogens, whereas salads presented the lowest occurrence. The vegetable category with highest incidence of Salmonella spp. (1.7%; 95% CI: 0.7–4.1%) and L. monocytogenes (2.2%; 95% CI: 1.0–4.7%) is leafy greens whilst STEC is more frequently recovered from sprouts (1.9%; 95% CI: 0.5–5.9%). In the case of fruits, the pooled prevalence estimates for Salmonella spp., L. monocytogenes and STEC were 1.60% (0.54%; 95% CI: 0.55–4.60%), 1.91% (0.50%; 95% CI: 0.93–3.88%) and 4.71% (1.52%; 95% CI: 1.73–12.2%), correspondingly.