Plant extracts are getting attention for their sterilizing, growth-promoting properties in the agricultural field. No exception exists when it comes to the treatment of propagating material with these natural components. Plant extracts may have complex compositions which affect plants or seeds in a positive way. However, they could also cause negative effects, like decreased germination, secondary metabolite contents or biomass gain. As the agricultural field requires sustainable techniques for plant growth and quality assurance in production, it is important to evaluate the potential effects of every alternative natural compound that shows promise for future plant treatment. Garlic (Allium sativum L.) is a popular spice crop grown in various regions of the world. Therefore, our study focused on an investigation of the early physiological and biochemical changes in garlic cloves (cv. ‘Jarus’ and ‘Vasariai’) treated with Thymus vulgaris essential oil and Syzygium aromaticum extract. Experiments were carried out in controlled climate conditions, in which the treated cloves were kept for four weeks. Results show that S. aromaticum extract increased germination in cv. ‘Jarus’ compared to untreated garlic cloves. Meanwhile, T. vulgaris caused lower germination of both cultivars compared to untreated cloves. None of the extracts increased biomass gain in garlic cloves. ABTS antioxidant activity was decreased by both extracts in cv. ‘Jarus’ (~7–47%) and ‘Vasariai’ (~22–32%) compared to untreated garlic cloves. Antioxidant DPPH and FRAP activities were ~6–11% and ~14–15% higher after ‘Vasariai’ treatment with extracts. Meanwhile, in ‘Jarus’ only, S. aromaticum extract caused an increase in DPPH and FRAP antioxidant activities. The elemental content was the highest in garlic cloves treated with T. vulgaris essential oil. Total phenolic compounds (TPC) and flavonoids (TF) were 1.2 times higher after S. aromaticum treatment of ‘Jarus’ compared to untreated cloves, while slightly increased TPC and two times higher TF values were found after treatment with T. vulgaris. Around 10% higher TPC and 1.5–3 times lower TF values were observed after the plant extract treatment of ‘Vasariai’ garlic cloves. Our study demonstrates initial changes in garlic cloves dependent on the plant extract treatment and cultivar. This provides important information for the future utilization of such technology, either alone or in combination with others.