In situ measurement of the bioavailability of organic pollutants in soil is crucial for understanding their environmental behavior and assessing health risks. Due to the high heterogeneity of soil, microscale determination is crucial for achieving high accuracy, but few methods are available. In this study, microsized probes coated with polydimethylsiloxane (PDMS) were used to measure the bioavailability of polycyclic aromatic hydrocarbons (PAHs) in soil in situ. The concentrations of PAHs enriched by the PDMS-coated probes correlated well with the results of bioassays using earthworms (R2 = 0.92–0.99) and ryegrass roots (R2 = 0.92–0.99). Compared with other chemical extraction methods, such as n-butanol extraction, the proposed method has advantages such as in situ operation, microvolume analysis, and negligible interference to the soil environment. In the soil rhizosphere zone, PAHs bioavailability decreased in the following order: rhizosphere > near-rhizosphere > far-rhizosphere. The bioavailability of PAHs in soil amended with biochar was also successfully characterized by the proposed method. Thus, this study developed an in situ and microscale method to predict the bioavailability of organic pollutants in contaminated soils and provides new insight into migration and transformation processes in rhizosphere soil.