Forest dieback due to increasingly frequent extreme climatic events, including droughts, poses a threat to ecosystem services provided by mountain forests. Yet, which biochemical pathways confer drought resilience or sensitivity in montane conifers is not fully understood. We analysed needles from 3-year-old Pinus sylvestris and Juniperus communis plants under a controlled, drought gradient, using untargeted GC-MS-based metabolite profiling, and targeted LC-MS/MS and HPLC analyses of hormones, antioxidants and lipid peroxidation products. In both species, indole-3-acetic acid (IAA), abscisic acid (ABA) and glutathione (GSH) increased with drought intensity, peaking at moderate drought in pine, but not until severe drought in juniper. Increasing drought severity was accompanied by increased glutathione disulphide (GSSG) concentrations in both species, and a decrease in GSH:GSSG ratio in pine. Lipid peroxidation markers, including trans-2-hexenal and 4-hydroxyhexenal, peaked under moderate drought in pine but accumulated progressively in juniper up to severe drought. Drought induced a steady increase in osmoregulatory sugars and proline in juniper, whereas pine predominantly accumulated amino acids, including serine, leucine and gamma-aminobutyric acid. In addition, drought induced species-specific responses in organic acids linked to the TCA cycle. Under severe drought, citrate and aconitic acid decreased, whereas fumarate and malic acid accumulated in juniper, while no significant changes occurred in pine. Our analysis reveals distinct species-specific metabolic responses to drought intensity, highlighting the complex biochemical mechanisms that may underlie differential resilience to water scarcity in montane conifers. Further effects of drought on primary metabolites and their downstream consequences for tree health are discussed.