This study evaluated the role of manure in mitigating drought stress and enhancing shallot (Allium ascalonicum L.) performance. A factorial randomized block design was implemented with three drought timings (early growth, vegetative, and bulb formation) and three manure doses (0, 10, and 20 t ha⁻¹). Results showed that the vegetative phase was the most drought-sensitive, with reductions of 55% in fresh biomass and 40% in dry biomass relative to the control. Leaf area declined by 49.2%, while plant length and leaf number decreased by 22–25%. Application of 20 t ha⁻¹ manure consistently alleviated drought effects across all stages, increasing biomass by 20–30% and bulb weight by up to 30.4% compared with unfertilized plants. Drought reduced bulb diameter by 14.5% during the vegetative phase, but this decline was mitigated to 10.5% with manure addition. These findings demonstrate that 20 t ha⁻¹ goat manure is an effective dose for improving shallot growth and yield under water deficit, providing a practical strategy to sustain production in drought-prone regions.