Background: Ectomycorrhizal (ECM and ECM-like) structures associated with plant root systems are a challenge for scientists. The dispersion pattern of roots within the soil profile and the nutritional conditions are both favourable factors to motivate the plants to make ECM associations. Results: This study discusses the colonization of mycorrhizal associations in Kobresia and Polygonum species including Polygonum viviparum, Kobresia filicina, K. myosuroides, Alnus nitida, Betula pendula, Pinus sylvestris, and Trifolium repens grown naturally in cold stressed soils of Gilgit-Baltistan (high-altitude alpine Deosai plains), Hazara, Swat, Dir, and Bajaur. Sieved soil batches were exposed to +5 °C (control), -10, -20, -30, -40, -50, -125 °C for 5 h, and selected plants were sown to these soils for 10 weeks under favourable conditions for ECM colonization. Ectomycorrhizal associations were examined in the above mentioned plants. Some ECM fungi have dark mycelia that look like the mantle and Hartig net. Examples of these are Kobresia filicina, K. myosuroides, and Polygonum viviparum. Findings of this study revealed that K. myosuroides excelled in ECM root tip length, dry mass, and NH4 concentration at -125 °C. Contrarily, A. nitida demonstrated the lower values, indicated its minimum tolerance. Notably, T. repens boasted the highest nitrogen concentration (18.7 ± 1.31 mg/g), while P. sylvestris led in phosphorus (3.2 ± 0.22 mg/g). The B. pendula showed the highest potassium concentration (9.4 ± 0.66 mg/g), emphasising species-specific nutrient uptake capabilities in extreme cold conditions. The PCA analysis revealed that the parameters, e.g., NH4 in soil mix (NH4), NO3 in soil mix (NO3), phosphorus in soil in species of Polygonum viviparum, Kobresia filicina, K. myosuroides, Alnus nitida, Betula pendula, Pinus sylvestris, and Trifolium repens are most accurately represented in cases of + 5 °C, -10 °C, and -20 °C temperatures. On the other hand, the parameters for ECM root tips (ECM) and Dry Mass (DM) are best described in -40 °C, -50 °C, and − 125 °C temperatures. All parameters have a strong influence on the variability of the system indicated the efficiency of ECM. The heatmap supported the nutrients positively correlated with ECM colonization with the host plants. Conclusion: At lower temperatures, hyphae and spores in roots were reduced, while soluble phosphorus concentrations of leaves were increased in cold stress soils. Maximum foliar nutrient concentrations were found in K. myosuroides at the lowest temperature treatments due to efficient functioning and colonization of ECM.