Autoimmune diseases, a term encompassing conditions where the immune system targets its own cells, consist of various pathologies, two of which are systemic lupus erythematosus (SLE) and mixed connective tissue disorder (MCTD). We present the unique case of an anti-ribonucleoprotein (RNP)-positive patient exhibiting renal pathology consistent with lupus nephritis and an additional collapsing variant of focal segmental glomerulonephropathy, who initially presented to the emergency department with signs and symptoms of pneumonia and portal vein thrombosis that were subsequently treated. Conflicting accounts of her autoimmune history led to an extensive workup during her stay, which yielded a tentative diagnosis of SLE vs. MCTD during her current hospitalization for pneumonia. The diagnostic labs revealed conflicting serological markers, with delayed anti-Smith positive results favoring lupus due to its high specificity. A subsequent renal biopsy showed complex renal involvement, suggesting SLE, despite initial positive anti-RNP antibodies known to be protective against renal pathology and classic for MCTD. Complicating matters further, the renal biopsy findings extended beyond common SLE pathology, including additional focal segmental glomerulonephritis (FSGS) involvement. Despite this uncertainty, the patient was treated as if solely having SLE, and immunosuppressives that could have been utilized for the possible MCTD component were avoided due to minimal signs of inflammation/immune response and normal kidney function. This case highlights the difficulty in accurately classifying lupus and MCTD, emphasizing the need for precise diagnosis for tailored patient care. Ongoing research is crucial to refine diagnostic criteria and improve patient outcomes.