Fungal genome sequencing has revealed the presence of multiple putative β-glucosidases; however, information regarding these new β-glucosidases is limited. A new β-glucosidase from Penicillium piceum, designated as PpCel3E, was first isolated and characterized. Using p-nitrophenyl-β-d-glucoside as substrate, PpCel3E showed the lowest Km among the β-glucosidases among all fungi studied. Moreover, PpCel3E exhibited a high transglycosylation activity of 1100 mg gentiobiose/mg and 142 mg sophorose/mg using glucose as the donor. PpCel3E is a novel bifunctional glycoside hydrolase with both β-glucosidase and β-xylosidase activity. Our results show that PpCel3E plays an important role in forming soluble cellulose inducer compounds, as well as in amplifying weak cellulase inducer signal and hemicellulase synthesis via its high transglycosylation activity. Supplementing PpCel3E at low concentrations (40 μg/g substrate) increased the saccharification efficiency of different cellulases by 20% to 27% by removing multiple inhibitors.