Ajwain (Trachyspermum ammi L.) Sprague is a high-value seed spice crop in India with considerable medicinal and culinary importance, yet its production is severely limited by stem rot caused by Sclerotinia sclerotiorum (Lib.) de Bary, resulting in yield losses exceeding 50–80 %, with major economic implications for farmers and the spice export market. This study tested the hypothesis that selected homoeopathic formulations can reproducibly suppress fungal growth, providing environmentally safe and economically viable alternatives to chemical fungicides. In vitro evaluation revealed complete inhibition of S. sclerotiorum by propiconazole 11.9 % + azoxystrobin 7.1 % (Apropo), tebuconazole 18.3 % + azoxystrobin 11 % (Custodia) and difenoconazole 11.4 % + azoxystrobin 18.2 % (Amistar Top) at 150 ppm, while hexaconazole 5 % emulsifiable concentrate (EC), propiconazole 25 % EC and azoxystrobin 23 % suspension concentrate (SC) showed substantial inhibition. Among homoeopathic treatments, Calcarea carbonica and Thuja occidentalis achieved over 70 % inhibition. By integrating experimental results with published literature, patents and prior studies, this work provides a robust, interdisciplinary framework connecting plant pathology, homoeopathy and sustainable agriculture. The findings reveal a breakthrough: ultra-diluted biological preparations can complement fungicides, reduce chemical dependency, mitigate resistance development and support low-input, organic and export-oriented spice production systems. Economically, adoption of these strategies could protect yield worth millions of USD annually, while minimising environmental and regulatory risks. Future research should focus on field validation, application optimisation, biochar integration and techno-economic modelling, ensuring global applicability and maximising agronomic, ecological and financial benefits.