The most devastating soilborne disease of soybean is Phytophthora root rot (PRR) caused by Phytophthora sojae. Biological control has emerged as an effective method of reducing soilborne diseases. The present study isolated the bacterial strain W82T‐44 from the rhizosphere soil of a resistant soybean variety Williams 82. This strain was identified as Bacillus amyloliquefaciens and exhibited a 92.4% inhibition of mycelial growth of P. sojae. W82T‐44 produced cellulase, siderophore and protease and significantly promoted soybean growth. W82T‐44 treatment, compared to the negative control, was found to significantly (p < 0.05) increase soybean plant height (22.34 vs. 18.47 cm), fresh weight of the whole plant (2.57 vs. 2.05 g), dry weight (0.43 vs. 0.32 g), total root length (266.80 vs. 182.53 cm), root area (27.10 vs. 17.84 cm2) and root volume (1.88 vs. 1.16 cm3). The fermentation filtrate of W82T‐44 had significant inhibitory effects on mycelial growth, oospore formation and cyst germination in P. sojae and additionally promoted zoospore encystment. W82T‐44 possessed genes involved in lipopeptide synthesis, including bacilysin, surfactin, fengycin and bacillomycin. Moreover, it significantly upregulated pathogenesis‐related genes (β‐1,3‐glucanase, nonexpressor of pathogenesis‐related gene 1, chitinase) and genes encoding defence enzymes (polyphenol oxidase, phenylalanine ammonia‐lyase, peroxidase) in soybean roots (p < 0.05). The PRR disease index of soybean treated with the W82T‐44 strain was significantly lower (11.67) than the negative control (40.00; p < 0.05). The present study indicates the potential of B. amyloliquefaciens W82T‐44 as a biological control agent against PRR from various perspectives.