Biotransformations catalysed by microbes are promising approach for producing a vast library of structurally diverse chemical molecules with applications in the pharmaceutical industry. The biotransformation of 11α-acetoxyprogesterone (1) by Phyllosticta sp. 16L1 has not been previously reported. In this study, the biotransformation of 11α-acetoxyprogesterone (1) was performed for the first time using the Phyllosticta sp. 16L1 strain. After an 8-day fermentation period, a new biotransformation metabolite, named as 11α-acetoxy-16α-hydroxyprogesterone (16α-hydroxy-3,20-dioxopregn-4-en-11α-yl acetate) (2) was isolated from the culture broth, along with its known isomer, 11α-acetoxy-15α-hydroxyprogesterone (3). The structure determination of the biotransformed products relied on comprehensive spectroscopic data, encompassing 1D and 2D-NMR, as well as LCMS analyses. The cytotoxic activity of the two biotransformed metabolites was assessed against selective human cancer cell lines, including hepatocellular carcinoma (HepG2), triple-negative breast cancer (MDA-MB-231), colorectal adenocarcinoma (Caco-2), and lung adenocarcinoma (A549). The results demonstrated that both metabolites 2 and 3 exhibited cytotoxic effects on the evaluated cell lines. Metabolite 2 showed stronger cytotoxic potential, with IC50 values ranging from 6.65 to 27.75 μM, while metabolite 3 displayed lower potency, with IC50 values between 38.20 and 162.53 μM. Notably, both metabolites exhibited minimal toxicity towards the normal liver Chang cells. Molecular docking studies were conducted to predict the binding modes and affinities of the metabolites against two targets (PDB: 5EM8 and 6V6O), both in 2D and 3D representations, with binding energies ranging from -8.5 to -7.2 kcal/mol. The results revealed that metabolites 2 and 3 interacted with key clinically significant amino acid residues, including Lys745, Met793, and Leu745, through conventional hydrogen bonding.