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This study addresses the growing need for phytoncide studies, driven by the demand to design indoor forest healing programs, including virtual reality experiences, for patients unable to visit actual forests. Previous studies have struggled to establish consistent phytoncide emission patterns in outdoor forest environments owing to varying microclimates and abiotic factors. In addition, the traditional gas chromatography–mass spectroscopy (GC-MS) method presents field measurement challenges, whereas the selected ion flow tube (SIFT)-MS method offers improved efficiency. This study concentrated on a controlled phytotron environment and compared the GC-MS and SIFT-MS findings, revealing similar emission trends with slightly higher SIFT-MS concentrations. Daily phytoncide emissions fluctuated with light intensity and abiotic stressors. Both methods consistently detected pinenes, primarily emitted by <i>Pinus strobus</i> L. seedlings, in the phytotron. Statistical analysis confirmed the compatibility between GC-MS and SIFT-MS results, supporting the use of SIFT-MS for forest phytoncide assessment. In the second phase, the phytoncide emissions were assessed indoors, outdoors, and in the phytotron, highlighting the superiority of the phytotron under controlled conditions. Despite certain limitations, this study underscores the value of phytotron-based measurements for indoor forest healing programs and the potential adoption of SIFT-MS in future field-based phytoncide research.