In line with green chemistry principles, a headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) method was developed and optimized to study the profile of biogenic volatile organic compounds (BVOCs) in soil samples from vineyards. The 75 µm CAR/PDMS fiber was selected for the identification of BVOCs in soil. The analytical method showed very good linearity (R2 ≥ 0.9914), sensitivity, and precision. Subsequently, soil matrix effect (ME) was examined on the BVOCs emission, through combined standard addition and internal standard (IS) calibration curves. The validated and optimized method was further applied in real soil samples from three vineyard areas of Cyprus (Omodos, Polemi, and Agros). Thirty-eight BVOCs were identified in total; among them acetone (0.65–5.96 μg/kg), hexane (0–0.50 μg/kg), heptane (0–0.18 μg/kg), trichloromethane (0.13–0.21 μg/kg), 1,2-dichloropropane (0.05–1.37 μg/kg), cyclohexane (0–0.26 μg/kg), benzene (0–0.51 μg/kg), toluene (0–0.54 μg/kg), p-xylene (0.15–0.97 μg/kg), and 1,3-di-tert-butyl-benzene (7.91–29.55 μg/kg) were quantified. The results revealed that the sampling vineyard location affects the BVOCs emissions in each soil. Also, vineyard elevation, soil pH, Ca, N, Zn, and Fe showed a significant correlation with the BVOCs emissions, which explains why vineyard soil regions are distinguished from each other, concluding that sample from Agros is the most abundant in BVOCs emissions.