This case report describes a 69-year-old woman with SLE and advanced chronic kidney disease who developed renal phospholipidosis (zebra bodies on electron microscopy) after 25 years of hydroxychloroquine therapy, with no evidence of Fabry disease. The phospholipidosis was absent in a biopsy 2.5 years earlier when renal function was better, suggesting that declining renal function may increase hydroxychloroquine accumulation and toxicity. Clinicians should consider drug-induced phospholipidosis in patients on hydroxychloroquine with worsening kidney function and weigh the risks of discontinuation against SLE activity.