Finding environmentally friendly solutions for crop growth and productivity has been gaining more attention recently. This meta-analysis aims to understand the combined application of arbuscular mycorrhizal fungi (AMF) and hydroponic systems compared to AMF in conventional (soil) systems. The analysis of up-to-date studies revealed that the root colonization, calculated as the proportion of colonized root segments relative to the total root length, by AMF in conventional (soil-based) culture exceeded hydroponic (or soilless) culture systems by 16.8%. The mean root colonization by AMF was determined to be 52.3% in hydroponic systems and 61.1% in conventional systems. Within hydroponic systems, the root colonization ranged from 2% to 20% after 10 days of inoculation, and notably, it exceeded 50% after 30 to 65 days, depending on the growing substrate and species. Under hydroponics, AMF application had a higher (compared to none-inoculated) positive effect on crop biomass and yield than fruit and leaf quality (antioxidants, phenols, and sugars) as well as leaf nutrients. However, AMF do not always have the potential to improve crop growth, quality and productivity in hydroponics. Among the studies analyzed in this review, approximately 34% (no effect: 29%; negative: 5%) reported no discernible positive effect on biomass or yield, 37% (no effect: 16%; negative: 21%) on fruit or leaf quality, and 60% (no effect: 47%; negative: 13%) on nutrient levels within plant tissues. To improve the performance of AMF in hydroponic systems, the meta-analysis recommended maintaining phosphorus levels in the nutrient solution within the range of 0.15 to 15.5 mg L−1 as elevated levels (40–75 mg L−1) were found to significantly reduce AMF colonization. Additionally, it was observed that certain hydroponic techniques, such as the presence of air bubbles generated by air pumps in floating hydroponic systems (Deep Flow technique) and continuous circulation of the nutrient solution (Ebb and Flow systems), may create dynamic conditions that could potentially hinder the introduction of AMF spores into hydroponic systems and potentially compromise the integrity of the spores and hyphae.