The present investigation was focused on the study of the chemical composition variability and biological activities of the essential oils from Clinopodium nepeta subsp. nepeta and subsp. glandulosum. Essential oils extraction was performed using hydrodistillation and the separation of the constituents was carried out by gas chromatography coupled with mass spectrometry (GC-MS). Antifungal activities were tested against Aspergillus flavus, Aspergillus terreus, Microsporum canis, Microsporum gypseum, Trichophyton mentagrophytes, and Candida albicans. Toxicity and repellency were evaluated against the stored product pests Tribolium confusum and Sitophilus zeamais. Both essential oils were characterized by a high content of oxygenated monoterpenes. Piperitone ranks first in the subspecies nepeta and piperitenone oxide is the dominant constituent in the subspecies glandulosum. All tested samples displayed noteworthy antifungal properties, with the highest activity observed for the essential oil of C. nepeta subsp. glandulosum, collected in Béni-M'tir, against T. mentagrophytes (MIC = 40 µg/mL). The essential oil samples of C. nepeta subsp. glandulosum were strongly repellent to the insect species (PR > 80%, after 2h) and highly toxic to S. zeamais reaching 97.5%-100% mortality after 24 h of exposure. In conclusion, this study showed considerable intra-specific changes in the quality of C. nepeta essential oils, which is reflected in different rates of antifungal and insecticidal activity.