Although factors initiating the inflammatory response to monosodium urate crystals have been identified, the role of the gut microbiota and their metabolites on gout remains unknown. This study aimed to investigate the changes in both gut microbiota and short-chain fatty acids (SCFAs) according to inflammatory states of gout in the same patients. This study enrolled 20 patients with gout in the acute state who had active joints and were followed up until the recovery state with no active joints. Blood and fecal samples were simultaneously collected within 3 days for each disease state. The stool microbiome was analyzed using 16S rRNA sequencing, and serum SCFAs were measured by gas chromatography-mass spectrometry. Differences in the gut microbiome and serum SCFAs were compared between the acute and recovery states. Beta diversity of the microbiome was significantly different between the acute and recovery states in terms of weighted UniFrac distance. In the recovery state, Prevotellaceae (p = 0.006) and the genus Prevotella (p = 0.009) were significantly enriched, whereas Enterobacteriaceae (p = 0.019) and its derivative genus Shigella (p = 0.023) were significantly decreased compared to the acute state. Similarly, the levels of acetate were dramatically increased in the recovery state compared to the acute state (p < 0.010). The levels of propionate and butyrate tended to increase but without statistical significance. Substantial alterations of bacterial composition with the promotion of SCFA formation (especially acetate) were found after treatment in patients with gouty arthritis.