Low protein rice can be part of a nutritionally adequate dietary pattern in the prevention of chronic kidney disease. We developed a low protein fermented genmai (brown rice) LPFG) to improve chronic kidney disease (CKD) management. The principal functional features of brown rice are retained in LPFG, lessening the negative spiral of gut-kidney associative spiral attributable to uremic dysbiosis and a leaky gut. LPFG is characterized by (1) an energy value the same as white rice, (2) a protein content less than 0.2 g/ 100 g, (3) a potassium content almost zero, (4) phosphorus less than a quarter that of conventional rice, (5) the presence of dietary fiber, (6) having γ-oryzanol, and (7) antioxidant activity. Dietary therapy for CKD patients is challenged by the joint needs to provide enough energy and to restrict protein. Patients replaced staple foods with LPFG without side dish restriction. Preliminary study of intervention with 3 months of LPFG reduced constipation probably by increased Blautia wexlerae, Bifidobacteria, acetic acid, and a decrease in potentially harmful bacteria. Protein intake decreased from 60 to 50 g per day. Urinary protein excretion decreased from 510 to 300 mg per day, and β2-microglobulin from 926 to 250 μg/L. Adherence to the LPFG diet enabled improvement in glomerular and tubular function.