<p>The production of greenhouse vegetables accounts for a considerable proportion of total vegetable production, and its percentage are still increasing. A substantial management practice input of unintentional heavy metals (HMs) into facility agriculture, which could lead to a serious pollution due to their relative low runoff. However, the bioaccumulation of HMs in a wide range of greenhouse vegetables and fruits and the impacts of soil properties on the bioaccumulation of HMs in facility agriculture are still unclear. In this study, the bioconcentration factor (BCF) of four HMs (Cd, Cr, Ni, and Pb) in 28 greenhouse fruits and vegetables was investigated among 468 plastic greenhouses in Beijing, China. Of these fruits and 4 group vegetables (i.e., leaf vegetables, fruit vegetables, root vegetables and legume vegetables), BCF_− Cr, BCF_− Pb, BCF_− Ni and BCF_− Cd are in the range of 0.0004–0.0006, 0.0006–0.0012, 0.0012–0.0028 and 0.0047–0.013, respectively. Pearson correlation analysis revealed that 22 soil properties have a significant correlation with the bioaccumulation of HMs at least in one crop. It was noteworthy that 6–13 soil properties explained 26.1–70.1% of the total variance for BCF_− Cd, BCF_− Cr, BCF_− Ni and BCF_− Pb in strawberry and 6 vegetables via redundancy analysis. Moreover, 7 soil properties have a significantly negative correlation with the bioaccumulation of 4 HMs. While, fine sand has a significantly positive correlation with the bioaccumulation of 4 HMs for rape, chilli pepper and cucumber. The results provide an important information into HMs accumulation in the edible parts of greenhouse vegetables and fruits and preliminarily elucidate soil properties on the bioaccumulation of HMs.</p> Graphical Abstract <p></p>