The Cladonio–Pinetum association is among Europe’s most endangered dry, sandy forest communities and is highly sensitive to microclimate and edaphic shifts. We quantified how seasonality and microhabitat (psammophilous grasslands vs. pine forests) modulate physiological traits of the dominant terricolous lichens Cladonia mitis and Cl. uncialis in Bory Tucholskie National Park (north-central Poland). From September 2022 to September 2023 we monitored six permanent sites, recording light, temperature, moisture, and soil chemistry, and seasonally measuring maximum quantum efficiency of PS II (FV/FM) and concentrations of usnic acid, total chlorophyll (a+b), lutein, and β-carotene. Usnic acid was quantified by UHPLC–PDA; chlorophylls/carotenoids by UHPLC–ESI-QqQ-MRM. FV/FM peaked in winter (0.77 ± 0.019) and reached a summer minimum (0.59 ± 0.05) in both species, consistent with photothermal and drought stress. Usnic acid showed the opposite pattern, peaking in summer (31.66 mg g⁻¹ DW) and remaining ∼2 × higher in Cl. mitis across seasons; beyond certain concentration levels, higher usnic acid content was associated with a downward trend in FV/FM. Total chlorophyll differed between species and was consistently higher in Cl. mitis; β-carotene showed seasonal variation, whereas lutein remained stable. Multiple regression identified light, air temperature, soil moisture, pH, and nitrogen as the main predictors of both FV/FM and usnic acid, explaining > 40% of their variance. Our results demonstrate that an integrated suite of chlorophyll fluorescence, pigment profiles, and secondary metabolite levels provides a sensitive early-warning system for detecting habitat degradation in Scots pine lichen forest. Managing canopy openness and curbing nutrient enrichment emerge as key conservation levers for sustaining these communities. Keywords: PS II efficiency (FV/FM); Usnic acid; Total chlorophyll (a+b); Lutein; β–carotene; Cladonio-Pinetum association.