This study examined the impact of organic manures from different sources (poultry, sheep, and cattle) on lemon balm (Melissa officinalis L., Lamiaceae) during different harvests. Manure application increased the photosynthetic pigments levels (chlorophyll-a, 9–41%; chlorophyll-b, 24–60%), biomass (41–60%), and essential oil yield (60–71%). Sheep manure treatment exhibited the highest antioxidant capacity among all the manures tested. Through GC-MS and GC-FID analysis, 10 chemical constituents were identified in the essential oil, accounting together for 91–95% of the total composition. The primary chemical component was geranial (39–46%), followed by neral (28–35%), (E)-caryophyllene (4.7–11%), geranyl acetate (2.7–5.9%), and caryophyllene oxide (1.7–4.8%). The utilization of livestock manures significantly improved the quality of the essential oil in terms of neral and geranial percentages compared to the control. Notably, during mid-August and early September, there was a substantial rise in these valuable compounds. However, a decrease in geranyl acetate and oxygenated monoterpenes resulted in a decline in the antioxidant capacity to 3%. Consequently, it is recommended to utilize essential oils from the second and third harvests for industrial purposes. Overall, the use of livestock manures, especially sheep manure, as a nutrient source for lemon balm cultivation proves to be a viable approach for producing high-quality essential oils.