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Bacterial urinary tract infections (UTIs) are common, ranging from benign cystitis to complicated pyelonephritis, which can lead to severe complications such as pyonephrosis and sepsis. Pyonephrosis, characterized by the presence of pus in the renal cavities, often requires urgent urological intervention. We report a unique case of pyonephrosis with a psoas abscess caused by Klebsiella pneumoniae (K. pneumoniae) and Peribacillus simplex (P. simplex) in a 64-year-old diabetic female patient. This is the first case of pyonephrosis caused by P. simplex. The patient presented with acute right lumbar pain, fever, and altered consciousness. Imaging revealed severe right hydronephrosis, pyonephrosis, and a perirenal phlegmon infiltrating the psoas with abscesses. Surgical drainage and nephrectomy were performed. Microbiological and proteomic analysis identified K. pneumoniae and P. simplex.This case highlights the importance of considering environmental bacteria like P. simplex in severe infections and ensuring rigorous protocols to avoid contamination. Successful management of pyonephrosis relies on prompt surgical drainage and appropriate antibiotic therapy based on culture results.