<p>Yersinia enterocolitica, a Gram-negative bacterium that can be transmitted through food, is among the leading pathogens responsible for human illness. Moreover, it is difficult to eliminate and poses a threat to human health because it can be refrigerated and is becoming resistant to traditional antibiotic treatments. A solution for this problem is the evaluation of natural bioactive molecules from Piper longum as potential inhibitors, which were studied via molecular docking, ADME/Tox profiling, and molecular dynamics simulations. The four ligands—Piperundecalidine, Fargesin, Aristolactam, and Pluviatilol—were tested for their binding affinity, pharmacokinetic properties, and ecological safety. Piperundecalidine was found to have the highest protein–ligand interactions and also formed strong hydrogen bonds with catalytically important residues, besides that it further continued to be stable throughout the 100 ns trajectory. Its ADME/Tox profiling showed the best pharmacokinetic profile, with high oral bioavailability (85%), strong intestinal absorption, blood–brain barrier penetration, and the lowest toxicity score (0.2) among the tested ligands. More importantly, Piperundecalidine was the only compound characterized as readily biodegradable, further confirming its ecological compatibility. The originality of this study is the combination of pharmacokinetic profiling with biodegradation analysis to isolate Piperundecalidine from Piper longum as a green natural bioactive agent against Y. enterocolitica. The results underscored the role of Piperundecalidine as a lead inhibitor and demonstrated the effectiveness of computational processes in natural product screening for antimicrobial drug development.</p>