The extensive use of synthetic agrochemicals has raised environmental and resistance concerns, underscoring the need for sustainable plant protection. Combining copper with plant-derived antimicrobials offers a promising alternative. Allicin (from garlic) and copper each possess broad-spectrum activity, and their combination may enhance efficacy while reducing toxicity. This study developed and evaluated a novel copper–allicin hybrid organic fertilizer–pesticide, assessing antimicrobial efficacy against major horticultural pathogens, effects on plant growth, yield, soil fertility, and impacts on soil microbial communities compared with conventional inputs. A pH-responsive copper–allicin complex was incorporated into a nutrient-rich compost matrix. In vitro activity against bacterial and fungal pathogens was evaluated using disk diffusion and minimum inhibitory concentration (MIC) assays. Field trials on citrus affected by citrus canker compared foliar application of the hybrid with copper oxychloride and untreated controls. Leaf micronutrients, yield components, soil copper, microbial diversity, and phytotoxicity (lettuce and radish) were measured. The hybrid exhibited broad-spectrum antimicrobial activity and strong synergy. In vitro, it inhibited 94.7% of Xanthomonas isolates and all 23 fungal strains, with MICs of 50–250 mg·l⁻¹, enabling an 80–90% reduction in copper relative to conventional rates. In field trials, it reduced citrus canker lesions by 97.4% (p < 0.01), outperforming copper oxychloride (82.1%). Treated trees showed increased leaf Cu and other micronutrients, resulting in 18.7% more fruit and 12.3% higher Brix (p < 0.01). Soil copper remained very low (≤0.08 ppm), while microbial diversity and plant growth were unaffected. Overall, the compost-based copper–allicin hybrid effectively suppressed phytopathogens, enhanced nutrition and yield, and maintained soil health. Its pH-responsive, slow-release design delivered potent antimicrobial action at substantially reduced copper levels, minimizing environmental toxicity. Superior field performance, improved fruit quality, minimal soil copper accumulation, and preserved soil microbiota confirm its potential as a sustainable, integrated fertilizer–pesticide for horticulture.