Natural nitrogen heterocycles biotransformation has been extensively used to prepare synthetic drugs and explore the fate of therapeutic agents inside the body. Herein, the ability of filamentous fungi to biotransform boldine and berberine was investigated. Docking simulation studies of boldine, berberine and their metabolites on the target enzymes: telomerase (TERT) and human protein tyrosine phosphatase 1B (PTP-1B) were also performed to investigate the anticancer and antidiabetic potentials of compounds in silico. The biotransformation of boldine and berberine with Cunninghamella elegans NRRL 2310, Rhodotorula rubra NRRL y1592, Penicillium chrysogeneum ATCC 10002, Cunninghamella blackesleeana MR198 and Cunninghamella blackesleeana NRRL 1369 via demethylation, N- oxidation, glucosidation, oxidation and hydroxylation reactions produced seven metabolites, namely: 1,10-didesmethyl-boldine (1), laurolitsine (2), 1,10-didesmethyl-norboldine (3), boldine-9-O-beta-D-glucoside (4), tridesmethyl berberine (5), demethylene berberine (6), and lambertine (7). Primarily, the structures of the metabolites were established by one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) analyses and mass spectrometry. In silico molecular docking simulation of the metabolites of boldine and berberine to the proteins TERT and PTP-1B, respectively, revealed good binding MolDock scores comparable to boldine and berberine and favorable interactions with the catalytic sites of the proteins. In conclusion, this study presented promising biologically prepared nitrogen scaffolds (isoquinolines) of boldine and berberine.