This study intended to improve physiological characteristics of Magnolia officinalis bark (MOB) extracts by Aspergillus niger fermentation. M. officinalis bark was extracted using distilled water, 95% ethanol, and methanol, and it was then fermented by A. niger. The physiological characteristics of the fermented extracts, namely, tyrosinase inhibitory activity, antioxidant activity, antibacterial activity, and anti-skin-aging activity, were evaluated and compared with those of unfermented extracts. To determine the safety of the fermented extracts, their cytotoxicity was analyzed by measuring the cell viability of CCD-966SK and human epidermal melanocytes (HEMn) after exposure. The fermented methanol extract exhibited the highest antityrosinase activity, total phenolic content, and antioxidant activity. The total phenolic content of the extracts fermented by A. niger was 3.52 times greater than that of the unfermented extracts. The optimal IC50 values for tyrosinase inhibition and 2,2-diphenyl-1-picrylhydrazyl (DPPH) removal by the A. niger-fermented extracts were 30 and 12 μg/mL, respectively. The fermented methanol extracts inhibited skin-aging-related enzymes such as collagenase, elastase, MMP-1, and MMP-2. Compared with the unfermented extracts, the fermented extracts also contained greater antibacterial activity against tested stains including MRSA. These results could be attributed to an increase in the concentration of original active compounds and the biosynthesis of new compounds during fermentation. In cytotoxicity assays, the A. niger-fermented extracts were nontoxic to CCD-966SK cells, even at 500 μg/mL. Hence, in general, methanol-extracted M. officinalis fermented by A. niger for 72 h has the most active antioxidant, skincare, or antiaging compounds for healthy food or cosmetics applications.