In recent years, occurrences of heat waves and drought have become increasingly frequent, highlighting the undeniable impact of climate change. The rise in temperatures and decline in rainfall have had severe repercussions on olive trees’ behavior and olive oil production. This study aims to evaluate the effects of two-year climate variations on olive oils from centenarian olive trees situated in the Côa Valley region of Northern Portugal. A selection of 25 centenarian plants was made, and the climate influence on fatty acid content, tocopherols, individual phenols, oxidative stability, and antioxidant activity was assessed over two consecutive years. During the second year of the study, a significant variation (p-value < 0.05) in the proportion of palmitic acid was observed, which increased from 12.9% to 13.6%. Conversely, stearic and arachidic acids exhibited a decrease from 2.7% to 2.3% and from 0.37% to 0.35%, respectively. Analysis of the oils revealed a noteworthy difference (p-value < 0.05) in the concentration of β-tocopherol. The concentration of oils derived from hydroxytyrosol and tyrosol significantly decreases (p-value < 0.005) during the second year. Additionally, significant differences (p-value < 0.005) were observed in the total phenol content and the percentage of ABTS inhibition, both of which decreased in the second year. These findings reinforce the notion that climatic conditions play a key role in shaping the composition of olive oils.