The aim of this study was to determine the influence of heavy metals on biological soil quality assessments in Vaccinium myrtillus L. rhizosphere soil as well as in non-rhizosphere soil from different polluted sites. The presented study was also conducted in order to determine any differences in the soil physicochemical and biological properties between the Vaccinium rhizosphere soil and the non-rhizosphere soil. The content of heavy metals and their potential bioavailability, content of macronutrients, physicochemical soil properties, activity of six soil enzymes and microarthropod communities were determined. Soil organic matter, the levels of C, N and all the studied macronutrients and almost all enzyme activity were significantly higher in the rhizosphere soil than in the non-rhizosphere soil. At the most contaminated site, the content of heavy metals was also higher in the rhizosphere soil, but their bioavailability was lower than in the non-rhizosphere soil. The β-glucosidase and urease activity in the soil correlated most negatively with the examined metals. The levels of two enzymes were also strongly impacted by the organic matter—the C and N levels and pH. The number of microarthropods as well as the QBS (soil biological quality index) and FEMI (abundance-based fauna index) were higher in the rhizosphere soil. The bilberry rhizosphere soil had stronger correlation coefficient values between the measured parameters than the non-rhizosphere soil, which suggests that rhizosphere soil is more sensitive and could be used in the monitoring and assessment of forest ecosystems. β-glucosidase and urease were the most sensitive indicators of the adverse impact of Cd, Zn and Pb. The FEMI index seems to be a better indicator than the QBS for identifying differences in soil quality.