Background <p>Understanding orchid mycorrhizas and symbiotic germination has long depended on in vitro models, yet these systems fail to capture the environmental forces shaping natural symbiosis. Here, we use RNA-seq to compare symbiotic and asymbiotic protocorms (the post-embryonic organ characteristic of orchid germination) grown in vitro with those developing in the field, allowing us to resolve how ecological context reshapes early plant physiology and plant-fungus interactions.</p> Results <p>Field-grown protocorms broadly aligned with the in vitro symbiotic model, while also showing how environmental signals refine a shared core transcriptional programme. Both symbiotic conditions showed transcriptomic patterns compatible with fungal colonisation but differed in the relative contribution of regulatory, transport, and stress-associated functions. Field protocorms showed stronger activation of membrane transport and wall-associated mechanosensing pathways, while sustaining defence-related regulation at a restrained, metabolically integrated level. Under in vitro conditions, symbiotic protocorms showed enhanced activation of stress-responsive and detoxification pathways compared with field-grown ones. The expression of light-associated plastid differentiation genes was attenuated despite brief culture-related illumination. In contrast, asymbiotic protocorms showed stronger activation of light- and oxidative-stress-related responses.</p> Conclusions <p>Together, these patterns indicate that field-grown protocorms show a more integrated and environmentally modulated transcriptional organisation, whereas in vitro symbiosis is associated with stress buffering and compensatory metabolic responses. By integrating field and laboratory datasets, this work provides a more complete portrait of early orchid symbiosis and protocorm physiology, clarifying both the interpretive power and limitations of current in vitro models.</p>