Using animal manure in organic systems can improve the quality of agricultural products, especially medicinal plants. In this study, the impact of different types and levels of animal manures on hyssop plant biomass and essential oil yield and profile was assessed. Three supply levels (Low, Medium, and High) were tested for poultry (Np), sheep (Ns), and cattle (Nc) manures. Through GC-MS and GC-FID analysis, 24 chemical constituents were identified in the hyssop essential oil, accounting for 93.7–97.8% of the total composition. The Medium-Nc and High-Np treatments had essential oil content ranging from 0.98% to 1.45%, significantly different from the control treatment at 1.17%. Essential oil yield in Low-Np, Medium-Np, and High-Np was 47.5, 53.8, and 49.2 kg ha−1, respectively, showing increases of 42.5%, 61.6%, and 47.7% compared to the control. Medium-Nc and High-Nc treatments had the most potent antioxidant properties compared to the control. Different amounts of poultry, sheep, and cattle manures led to distinct differences in essential oil compounds, categorizing the manure treatments into three groups. Medium-Np had 44% more air-dried biomass than the control, while no significant difference was found in air-dried herbal product levels among sheep and cattle manures. Taken together, farmers focusing on biomass and essential oil should opt for Medium poultry manure. The pharmaceutical industry should explore other fertilizer options based on secondary metabolite needs.