Microbial biotransformation has become a tool of great importance in the modification of compounds for chemical, pharmaceutical and agrochemical industries, due to the high chemo-, regio- and stereoselectivity provided by the enzymes generated in situ. Laccases are oxidoreductase-type enzymes and occur in fungi, bacteria, and plants. Such enzymes are capable of oxidizing electron-rich substrates, including various phenolic compounds and aromatic amines. Laccases produced by Trametes versicolor (Tvlac) have one of the greatest redox potentials and constitute the main extracellular components of the fungus. The aim of the present study was to comprehensively evaluate the biotransformation of methyl p-coumarate (1a), methyl ferulate (2a), and methyl caffeate (3a) by Trametes versicolor ATCC 200801. For this, 5 mg of each substrate (1a, 2a and 3a) were solubilized in 350 μL of DMSO and added to Erlenmeyer flasks holding 50 mL of fermentation medium (0.2% glucose, 0.2% malt extract, 0.1% peptone, 0.1% Tween 80, 0.0005% copper (II) sulfate, pH 5.5), and five 6- mm disks containing mycelia. The biotransformation experiments were carried out at 28 °C for 72 h under stirring at 120 rpm. All the experiments were performed in triplicate. Samples were taken daily until the finish of the experiment. Additionally, molecular docking analysis was performed to study the interactions between the substrates with Tvlac active sites, by using the AutoDock v.4.2 software where the Lamarckian genetic algorithm (LGA) is implemented. The biotransformation results showed that only the substrate 1a was derivatized under the evaluated conditions. The crude extracts of the biotransformations were analyzed by HPLC-DAD, indicating the formation of metabolites 1, 1b and 3a. The molecular docking analysis showed different variations of Gibbs free energy (ΔG) for substrates 1a, 2a and 3a, with values of -6.39, -7.37 and -7.55 kcal/mol, respectively. The lower ΔG value obtained for 1a indicated greater reactivity (less stability) in comparison with 2a and 3a, justifying the formation of derivatives from 1a. In summary, our results showed that the position and type of substituents in the aromatic ring of phenolic substrates influenced their conformation and orientation at the Tvlac site. Substrates that contained two substituents on the aromatic ring (methyl ferulate and methyl caffeate) displayed additional hydrogen-bonding interactions with Tvlac, which increased the stability of the Tvlac-substrate complexes and prevented the biotransformation occurrence.