The development of safer opioid therapeutics remains an urgent challenge, given the limitations and adverse effects of current μ-opioid receptor (MOR) agonists. Natural products such as mitragynine, the predominant alkaloid from Mitragyna speciosa (kratom), provide structurally complex scaffolds for probing MOR signaling bias and structure-activity relationships. However, enzymatic strategies for mitragynine modification remain largely restricted to native plant or non-native eukaryotic enzymes, which are often insoluble, low-yielding, or incompatible with heterologous expression, limiting their use for late-stage derivatization. Here, we establish a modular biocatalytic platform that repurposes noncognate oxidative enzymes for in vivo diversification of mitragynine. Using flavin-dependent monooxygenases (CtdE) and an orphan halogenase (D3) from Saccharophagus degradans, we achieved site-selective N-oxidation and C10 bromination, respectively, and demonstrate that these reactions can be combined in a single Escherichia coli host to perform sequential halogenation and oxidation directly from the parent alkaloid. The resulting analogues, including 10-bromo-mitragynine and its N-oxide, exhibit distinct MOR binding and G protein signaling profiles while failing to recruit β-arrestin. Collectively, these findings introduce a generalizable whole-cell platform for programmable, multistep alkaloid functionalization and highlight how biocatalysis can drive pharmacology to guide the discovery of novel bioactive scaffolds.