The phytochemical profiling of hemp inflorescences of clonal plants growing in different conditions related to altitude was investigated. Four strains of industrial hemp (Cannabis sativa L., family Cannabaceae) of Kompolti variety were selected and cloned to provide genetically uniform material for analyses of secondary metabolites (terpenes, cannabinoids, and flavonoids) at two different elevations: mountain (Alagna Valsesia 1200 m ASL) and plains (Vercelli Province 130 m ASL). Environmental conditions influenced by elevation have proven to be important factors inducing variations in hemp inflorescences’ secondary metabolite composition. In fact, all plants grown at altitude exhibited a higher total amount of terpenes when compared with plains counterparts, with β-Myrcene, trans-Caryophyllene and α-Humulene as the main contributors. A metabolomic, un-targeted approach performed by HPLC-Q-Exactive-Orbitrap®-MS platform with subsequent data processing performed by Compound Discoverer™ software, was crucial for the appropriate recognition of many metabolites, clearly distinguishing mountain from plains specimens. Cannabidiolic acid CBDA was the most abundant phytocannabinoid, with significantly higher concentrations in the mountain samples. The metabolic pathway of CBGA (considered as the progenitor/precursor of all cannabinoids) was also activated towards the production of CBCA, which occurs in considerably 3 times higher quantities than in the clones grown at high altitude. Isoprenoid flavones (Cannaflavins A, B, and C) were correspondingly upregulated in mountain samples, while apigenin turned out to be more abundant in plains samples. The possibility to use hemp inflorescences in pharmaceutical/nutraceutical applications opens new challenges to understand how hemp crops respond in terms of secondary metabolite production in various environments. In this regard, our results with the applied analytical strategy may constitute an effective way of phytochemical profiling hemp inflorescences.