Fresh Gastrodia elata tubers are highly perishable after harvest because pathogen infection accelerates quality deterioration and limits their storage and commercial utilisation. This study examined lesion development in wounded, pathogen-inoculated tubers held at 24 ± 1 °C and, in a separate experiment, quality and physiological changes in non-inoculated tubers stored at 4 ± 1 °C. In the inoculation assay, 1 mM salicylic acid (SA) reduced lesion development following inoculation with Fusarium sp. (isolate 1022-1-1) and Aspergillus sp. (isolate 1022-11). During cold storage, SA-treated tubers maintained higher soluble solid content and showed less weight loss, membrane permeability, and malondialdehyde accumulation than controls. SA application promoted the enzymatic activities and transcriptional expression of superoxide dismutase, catalase, and peroxidase. It also activated the ascorbate–glutathione cycle by promoting ascorbic acid and glutathione accumulation, along with increasing the enzymatic activities and transcript abundance of several cycle-related enzymes, including ascorbate peroxidase, glutathione reductase, monodehydroascorbate reductase, and dehydroascorbate reductase. These responses limited superoxide anion production and excessive hydrogen peroxide accumulation, thereby alleviating oxidative damage. SA enhanced phenylpropanoid metabolism through the upregulation of phenylalanine ammonia-lyase, cinnamate 4-hydroxylase, and 4-coumaroyl-CoA ligase at both enzymatic and transcriptional levels, contributing to increased levels of total phenolics, flavonoids, and lignin. Furthermore, SA contributed to ATP maintenance by upregulating hexokinase, succinate dehydrogenase, cytochrome c oxidase, H⁺-ATPase, and Ca²⁺-ATPase at both enzymatic and transcriptional levels. Overall, SA treatment reduced lesion development in inoculated G. elata tubers and helped maintain the quality of non-inoculated tubers during cold storage.