Root-knot nematode (RKN) is a serious threat to crops worldwide due to the difficulty in controlling it and the limited eco-friendly alternatives to deal with the biotic stress it causes. In the present work, water-extractable fractions obtained from vermicompost (WSFv), vermicompost enriched with Trichoderma asperellum (WSFta) and T. virens (WSFtv) were tested as biotechnological tools to reduce the impacts of RKN on gas exchange, water use efficiency (WUE) and nutrient concentration in tomato and bell pepper plants. The plants were infected with 5000 eggs and eventual J2 of RKN and then treated with the water-extractable fractions for seven weeks. It was observed that the addition of WSFta, WSFtv and WSFv increased the CO2 assimilation, stomatal conductance and WUE in the tomato plants. In the bell pepper plants, WSFta, WSFtv, WSFv increased the stomatal conductance, while WUE was higher in the treatment with WSFtv. In fact, the parameters associated with the gas exchange were usually higher in the bell pepper than in the tomato plants. Overall, higher contents of N, Mg, B and Mn were detected when the extracts were applied in both bell pepper and tomato plants. The application of the water-extractable fractions, inoculated or not with Trichoderma, attenuates the RKN damage on the gas exchange parameters and successfully enhanced the nutrient concentration in the infected tomato and bell pepper plants, showing that it could be an important and promising tool for reducing the damage caused by this pathogen. We suggest that both the tomato and pepper plants can cope with the dilemma between growth and stress response via stomata regulation that are modulated by the WSF and Trichoderma.