Endophytic fungi can harbor extensive biosynthetic capacity, yet natural-product discovery commonly interrogates them after removal from the host and transfer to simplified culture. This creates a central uncertainty: chemistry observed ex planta may represent only one state within a larger, interaction-dependent chemical repertoire. This integrative review synthesized ecological, metabolomic, genomic, regulatory, co-culture, and pathway-activation evidence relevant to endophyte chemical expression. A targeted evidence-selection process screened 52 unique DOI-resolved candidate articles, assessed 42 in detail, and retained 36 for synthesis. Evidence types were kept distinct to avoid treating metabolite detection, structural assignment, biosynthetic attribution, and ecological function as equivalent. The literature supports four recurring patterns. First, host-associated and isolated-culture chemical profiles can diverge. Second, host chemistry, microbial competitors, environmental stress, and fungal regulatory state can alter the context in which metabolites or biosynthetic gene clusters are expressed. Third, co-culture and engineered activation can expose chemistry not evident under standard monoculture, but these interventions do not necessarily reproduce native host cues. Fourth, genome mining and metabolomics strengthen discovery when combined, yet assignment confidence increases only through orthogonal validation. We therefore propose an evidence-bounded view of endophyte discovery in which ecological perturbation generates hypotheses, biosynthetic and analytical tools constrain source and structure, and functional interpretation remains a separate validation problem. Endophyte–host chemical ecology is best treated as a conditional discovery space rather than a fixed inventory. Its value lies in experimentally testing context-dependent chemistry while preserving uncertainty about source, mechanism, transferability, and ecological function.
