15 participants (5 females, 10 males) showed varying degrees of urinary protein reduction post-treatment; 6 with >50% decrease, 9 with <50%. Mean 24-h urinary protein quantification pre-enrollment was 1.15 ± 0.94 g/day. Gastrointestinal symptoms improved in all post-treatment. 24-h urinary protein quantification decreased significantly at 1 and 3 months post-FMT, excluding 2 with acute infections. Specific urinary proteins and most immune cells/cytokines showed no significant changes. B cell counts decreased significantly post-FMT. Safety indicators showed no significant changes except for serum sodium and calcium. No severe adverse events reported. Gut microbiota composition changed post-FMT, with correlations noted between specific bacteria and B cell changes. Intestinal metabolite composition also changed, with correlations found between specific metabolites and B cells, serum calcium, and sodium.