Increasing prices and market demand for organic products are stimulants of organic farming. However, this sector is a challenge for producers and further improvements are still necessary. The present study case was conducted to compare the effects of organic (OF) and conventional (CF) farming on lavender (Lavandula angustifolia Mill.) oil yield, plant pigments and essential oil composition. The study was conducted for two years in the period 2019–2020. Six private farms were included in the experiment with conventional and organic agriculture systems. They are located in Kazanlak Valley, Southern Bulgaria. Organic lavender inflorescences were determined to have chlorophyll a and total chlorophyll within a narrow range between 251.3 and 275.7 μg·g−1 and between 375.5 and 487.0 μg·g−1 compared to conventional ones—between 245.9 and 377.5 μg·g−1 and 385.3 and 595.4 μg·g−1 respectively. However, carotenoids and anthocyanins were in a wide range in organic lavender between 36.9 and 72.2 μg·g−1 and 410 and 1240 µg cyn-3-gly.g−1 compared to conventional ones—between 55.5 and 77.3 μg·g−1 and 200 and 780 µg cyn-3-gly.g−1, respectively, for both studied years. The key constituents in essential oil were linalyl acetate (28.42–38.23%), linalool (20.01–31.04%) and β-caryophyllene (7.95–14.97%). The composition was compared with the parameters set out in the international standard for lavender oil. The influence of the type of agricultural system on essential oil yield and its composition was not found. According to the obtained results, levels of chlorophyll a, chlorophyll b and total chlorophyll were higher in conventional farming than in organic farming for the second year of the study.