Can endometriosis cause protein to show up in urine?

Very unlikely; rare: Endometriotic implants have been reported in many sites outside the pelvic and abdominal cavity (like the lungs, the umbilicus, skin, cervix...) They may theoretically extend to the bladder and therefore could very rarely account for or "cause protein to show up in urine". A cystoscopic exam or a urine cytologic test for endometrial cells and hemosiderin deposits may help answer your question.