How would you manage a patient with CKD4 due to lupus nephritis of unknown class who develops AKI requiring hemodialysis and nephrotic range proteinuria and is found to have atrophic kidneys on imaging?

The decision to biopsy a kidney is not based just on size.

The operator should look at the kidney size compared to the height of the patient and the echogenicity on ultrasound.

If the patient is short with a normal/near-normal echogenicity, even a <9cm kidney can yield useful information. This is relevant especially in AKI (assuming the kidney function was recently normal) where a reversible etiology of kidney failure may be present.

In a small series of patients with kidney sizes between 6-9 cm, useful information was obtained in the majority.

El-Reshaid et al., PMID 28352011

In a patient with “CKD4” and atrophic kidneys, I suspect risk would outweigh potential benefit, particularly if Kbx was already done in the past to confirm “lupus nephritis.” However, as it also states “unknown class” (which I think implies no prior biopsy), one could hedge towards needing a complete picture for future reference, such as after transplant.

I agree with above and would proceed to biopsy. In addition, some may consider the risk of renal biopsy increased as relates to atrophic appearance however generally this alone would not pose additional risk of bleeding (provided adequate visualization of the kidney is possible). Although cortical thickness certainly correlates with chronic and irreversible kidney injury with expected poor response to treatment, echogenicity is less reliable as this can also be observed in acute kidney injury and is commonly seen in lupus nephritis.

Rijnink et al., PMID 28473317