Abstract: The understanding of plant-associated bacterial communities has attracted a lot of attention because of their crucial function in improving plant physiology and productivity. These benefits include bioremediation, nutrient solubilization, and stress tolerance. Notably, the use of bacteria as probiotics in eco-efficient plant growing systems (EPGS), including hydroponics and aquaponics, is emerging. These systems are ecologically friendly, productive, resource-efficient, and hold excellent promises for a more sustainable agriculture. This review explores the use of probiotics in the unique stages of plant growth in EPGS, highlighting the significance of managing nutrients and conditions for the plant growth. Moreover, it clarifies how important bacteria are to the nitrogen cycle in EPGS, particularly nitrifying and nitrogen-fixing species. Furthermore, it discusses the methods for bioprospecting new probiotics, highlighting the importance of the combination of metagenomics and conventional microbiology methods. It also highlights how crucial it is to understand the dynamics of probiotics in EPGS for environmentally friendly plant production and preservation in the face of climate change.