The genus Pseudomonas harbours numerous strains that positively affect plant growth and defence through diverse mechanisms such as nutrient solubilisation and production of phytohormones or secondary metabolites. The aim of this study was to compare the impact of six plant-beneficial Pseudomonas strains on tomato (Solanum lycopersicum) growth and holobiont physiology. The physiological impact was determined by profiling the activities of key enzymes in the central carbohydrate and antioxidant metabolism. Root inoculation of tomato seedlings with Pseudomonas strains in a greenhouse experiment induced plant growth, measured as biomass and plant height promotion. The bacterial strains also increased leaf chlorophyll content and caused distinct carbohydrate and antioxidative metabolism enzyme activity profiles in leaf and root tissue respectively. For the carbohydrate metabolism, the activities of several key enzymes involved in assimilate partitioning from source to sink and processing of the transport sugar sucrose for catabolism and anabolism were stimulated. For the antioxidative metabolism, both enzymes involved in detoxification of reactive oxygen species and redox buffering were increased. These increased enzyme activities in response to bacterial inoculation could contribute to balancing plant growth and defence. Importantly, positive correlations between plant growth parameters and distinct enzyme activities suggest that host plant biosignatures may be predicting bacteria with plant growth-promoting potential. These findings offer new perspectives for integrating physiological fingerprinting in the screening of microbes during early developmental stages of the host plant. In addition, determining plant metabolic biosignatures could be a rapid tool for predicting the potential and improvement of stress resiliency.