Bile salts, phospholipids, and digestive proteins are amphipathic compounds found naturally in the human gastrointestinal system. Therefore, it is important to consider their effects on the crystallization kinetics and solution behaviour of drugs intended for oral delivery. Supersaturating drug delivery systems that employ high energy solid forms and polymeric additives are often hailed as the gold standard for increasing drug concentration in the gastrointestinal system. However, the effects of amphiphilic compounds present in the gastrointestinal system on the crystallization behaviour of these systems are often overlooked. In this study, the effects of bile salts, phospholipids, mixtures of phospholipid and bile salts as well as digestive proteins on the crystallization kinetics of the antimicrobial agent clofazimine (CFZ) were evaluated. The crystallization inhibitory properties of these gastrointestinal amphiphiles were compared with commonly used synthetic polymers, and several of these amphipathic gastrointestinal compounds showed promise as crystallization inhibitors of clofazimine hydrochloride during induction time experiments. The best crystallization inhibitors from this induction time screening were then compared as solid physical mixtures in modified fasted state simulated gastric fluid (m-FaSSGF). Here it was found that heterogeneous nucleation of CFZ hydrochloride onto the dissolving surface of CFZ solid forms prevented these additives from inhibiting crystallization in this biorelevant media. This heterogeneous nucleation of CFZ hydrochloride was monitored in real time, using optical microscopic techniques.