The susceptibility of apples to post-harvest decay by the fungus Botrytis cinerea has prompted innovative research into alternative preservation methods. In this regard, essential oils (EOs) have emerged as promising candidates due to their natural origin and potential antimicrobial properties. Investigating the biological significance of EO blends is crucial for understanding their potential antimicrobial mechanisms and evaluating their capacity to modulate metabolic responses that could inhibit post-harvest fungal decay in fruit tissues. This study delves into the intricate chemistry of apples when subjected to various EO treatments, shedding light on the profound changes in alcohols, esters, C6 compounds, terpenes, and volatile compounds. Based on our results, terpene concentrations exhibit significant variations with α-Pinene ranging from 13.4 µg L−1 in Fungus + Thymol + 1,8-Cineole treatment (Fun+Thy+Cin) to 28.7 µg L−1 in Fungus + Thymol + 1,8-Cineole + Eugenol treatment (Fun+Thy+Cin+Eug), and β-Pinene concentrations spanning 19.3 µg L−1 in Fungus + 1,8-Cineole + Eugenol treatment (Fun+Cin+Eug) to 45.5 µg L−1 in Fungus + Thymol + 1,8-Cineole + Eugenol treatment (Fun+Thy+Cin+Eug). Ester elaboration presents marked changes, with ethyl octanoate peaking at 715.7 µg L−1 in Fungus + Thymol + 1,8-Cineole + Eugenol treatment (Fun+Thy+Cin+Eug) and ethyl propionate reaching 152.9 µg L−1 in Fungus + Thymol treatment (Fun+Thy). The volatile compound dynamics also demonstrate significant variations, with hexanoic acid concentrations ranging from 0.1 to 0.2 among treatments and 3-Methylbutanal displaying concentrations from 0.8 to 6.4, with the highest concentration observed in the Control. The essential oil combination of Thymol, Eugenol, and 1,8-Cineol (Fun+Thy+Cin+Eug) had the most significant impact on the volatile compound content in the fruits. The findings from this study unveil the intricate responses of apple chemistry to various EO treatments. These insights hold promise for enhancing post-harvest apple preservation strategies through the modulation of EO treatments.