This study demonstrates how integrating transmembrane and paracellular transport mechanisms improves prediction of human oral bioavailability for amphoteric drugs. Using PAMPA at pH 6.5 and incorporating a generalized Caco-2–based paracellular model, the authors created an “in-combo” permeability approach that closely aligned with observed clinical bioavailability data. The results highlight that many low-bioavailability ampholytes—particularly zwitterionic compounds—rely heavily on paracellular transport, even at molecular weights above 350 Da. The analysis also underscores the importance of considering nonpassive transport, metabolic instability, and microclimate pH effects when interpreting permeability data and forecasting in vivo performance.