<p>Permanent cover crops offer multiple benefits, including improved soil and plant health and reduced use of agrochemicals. This study examined the impact of under-vine soil management—herbicide weeding (HW) vs. permanent cover crop (PCC) with <i>Festuca arundinacea</i>—on Botrytis Bunch Rot (BBR) caused by <i>Botrytis cinerea</i>, and potential plant defense mechanisms involved. The experiment was conducted in an irrigated experimental vineyard of Tannat grapevines grafted onto SO4, where HW and PCC treatments had been established for more than 10 years. During the 2020/2021 season, BBR incidence and severity, disease progression in inoculated leaves, levels of phytoalexins and antioxidant activity in leaves and berries, berry skin anatomy and rhizosphere microbial communities were evaluated. PCC was associated with lower BBR incidence (<i>p</i> = 0.001) and intensity (<i>p</i> &lt; 0.001) for visible symptoms and latent infections (<i>p</i> = 0.002), and reduced disease progression in inoculated leaves (<i>p</i> &lt; 0.001). Berries from PCC exhibited thicker cuticle (<i>p</i> &lt; 0.001) and epidermis (<i>p</i> = 0.008), higher total polyphenol content in leaves (<i>p</i> = 0.01) and increased ascorbate peroxidase activity in berry skin (<i>p</i> &lt; 0.001). Distinct microbial community compositions were observed at harvest, with differential taxa identified as indicators of each soil management, with a higher abundance of potentially beneficial bacteria in PCC. The enhanced response of grapevines to BBR under PCC management likely results from the combined effect of multiple factors.</p>