Erysimum croceum is a rare, endemic, and medicinally valuable plant listed in Kazakhstan’s Red Data Book. Employing modern geobotanical and floristic, soil methods, four natural populations of the rare endemic species Erysimum croceum were identified and comprehensively assessed in the Zailiyskiy Alatau region of the northern Tien Shan. The studied populations are located in distinct ecological settings: one in the Big Almaty gorge, two on the opposite banks of the Small Almaty gorge, and one in the Issyk gorge. Comprehensive field surveys were conducted to characterize their plant communities, population structure, and soil properties. The presence of flowering and fruiting individuals indicates that these populations currently maintain reproductive viability within the protected spruce forest belt at elevations of 1,724–2,597 m a.s.l. However, the absence of juvenile and immature individuals in three of the four populations indicates limited regeneration and classifies them as regressive, which could pose a risk of gradual decline. Comparative soil analyses revealed notable differences: mountain dark forest soils of populations 1 and 2 showed moderate organic matter (up to 12.7%) and favorable nutrient levels, while population 4 demonstrated the highest ecological potential, with humus content up to 32.16% and a fine dusty loam texture supporting high water retention and biodiversity. The population near Issyk gorge is particularly vulnerable to tourist pressure. Implement long-term demographic monitoring across all sites, regulate visitor access and protect high-quality microsites (notably near Issyk), and establish ex-situ safeguards through seed banking and botanical-garden cultivation; restoration should target humus-rich, medium-loam reference conditions. This study provides the first integrated eco-phytocoenotic and edaphic assessment across four E. croceum populations in the Northern Tien Shan, quantitatively linking soil heterogeneity to population status and delivering site-specific conservation guidance.