Abstract: Accumulation of heavy metal cadmium (Cd) in vegetable field soils poses significant concerns owing to various pathways. Excessive Cd not only induces severe toxicity in animals and plants but also poses substantial risks to human health through the food chain. Biological toxicity and Cd accumulation in organisms are influenced not only by the total amount of Cd in the soil, but also by its activity. Under the influence of crop roots, various soil microorganisms affect the migration, release, and absorption of Cd in multiple ways. Current research on soil Cd availability and microorganisms has primarily focused on identifying Cd-resistant bacteria in soil and enhancing Cd-contaminated soil phytoremediation by introducing external microorganisms. However, native microorganisms are abundant, and comprehensive data on how their combination with different Cd-accumulating crops affects Cd bioavailability, plant absorption and accumulation characteristics are lacking. In particular, it remains unclear whether the combination of various Cd-accumulation varieties of solanaceous fruits and their native microorganisms influence soil Cd bioavailability, thereby affecting variations in Cd absorption and accumulation. The accumulation of Cd in crops is primarily determined by its availability in the soil. In the early stages, our research group selected tomato varieties with high Cd accumulation (‘Hezuo 908’) and low Cd accumulation (‘Provence’). Through solution culture experiments, we found that ‘Hezuo 908’ had a greater effect on the activation of insoluble Cd than ‘Provence’. To address the issue of Cd accumulation and ensure crop safety, our study focused on ‘Provence’ and ‘Hezuo 908’ tomato varieties. Using Illumina MiSeq sequencing, we investigated the effects of tomatoes and indigenous microorganisms on soil available Cd levels and microbial diversity. The experiment involved treating the background soil (with 0.24 mg∙kg⁻¹ Cd) and Cd-contaminated soil (with 0.60 mg∙kg⁻¹ Cd) with (without indigenous microorganisms) and without sterilization (containing indigenous microorganisms). Subsequently, ‘Hezuo 908’ and ‘Provence’ were planted separately. The results indicated that ‘Hezuo 908’ had a significantly higher capacity to absorb and accumulate soil Cd compared to ‘Provence’ in both types of soil. Planting ‘Provence’ and ‘Hezuo 908’ in sterilized soil increased the available Cd content in contaminated soil by 3.16% and 5.26%, respectively, compared to the control group with no planting. Moreover, the presence of indigenous microorganisms in unsterilized soil led to a 27.37% increase in available Cd in contaminated soil. When ‘Provence’ or ‘Hezuo 908’ were planted in non-sterilized soil alongside indigenous microorganisms, the available Cd content in soil increased by 29.59% or 28.00%, respectively, compared to single crop planting, and by 4.96% or 5.79%, respectively, compared to the sole presence of indigenous microorganisms. Compared with the control treatment, planting ‘Provence’ and ‘Hezuo 908’ in unsterilized contaminated soil significantly increased the relative abundance of Sphingomonas, Microcoleus, Haliangium, and Herpetosiphon. Additionally, the relative abundances of Actinoplanes and Nitrospira increased in the non-sterile soil planting ‘Provence’ treatment, while Hydrogenophaga and Lysobacter increased in the non-sterile contaminated soil planting ‘Hezuo 908’ treatment, demonstrating distinct differences among the bacteria genuses. These dominant bacteria may be linked to the varying available Cd content in the soil planted with the two tomato varieties. In conclusion, the combined effects of these tomato varieties and indigenous microorganisms enhanced soil microorganism diversity, altered the community structure of soil bacteria, and notably increased the available Cd content in soil.