Abstract Gastrointestinal first‐pass metabolism plays an important role in bioavailability and in drug–drug interactions. Physiologically‐based pharmacokinetic (PBPK) modeling is a powerful tool to integrate these processes mechanistically. However, a correct bottom‐up prediction of GI first‐pass metabolism is challenging and depends on various model parameters like the level of enzyme expression and the basolateral intestinal mucosa permeability ( P mucosa ). This work aimed to investigate if cytochrome P450 (CYP) 3A4 expression could help predict the first‐pass effect using PBPK modeling or whether additional factors like P mucosa do play additional roles using PBPK modeling. To this end, a systematic review of the absolute CYP3A expression in the human gastrointestinal tract and liver was conducted. The resulting CYP3A4 expression profile and two previously published profiles were applied to PBPK models of seven CYP3A4 substrates (alfentanil, alprazolam, felodipine, midazolam, sildenafil, triazolam, and verapamil) built‐in PK‐Sim®. For each compound, it was assessed whether first‐pass metabolism could be adequately predicted based on the integrated CYP3A4 expression profile alone or whether an optimization of P mucosa was required. Evaluation criteria were the precision of the predicted interstudy bioavailabilities and area under the concentration–time curves. It was found that none of the expression profiles provided upfront an adequate description of the extent of GI metabolism and that optimization of P mucosa as a compound‐specific parameter improved the prediction of most models. Our findings indicate that a pure bottom‐up prediction of gastrointestinal first‐pass metabolism is currently not possible and that compound‐specific features like P mucosa must be considered as well.