Data reduction and correction steps and processed data reproducibility in the emerging single‐crystal total‐scattering‐based technique of three‐dimensional differential atomic pair distribution function (3D‐ΔPDF) analysis are explored. All steps from sample measurement to data processing are outlined using a crystal of CuIr2S4 as an example, studied in a setup equipped with a high‐energy X‐ray beam and a flat‐panel area detector. Computational overhead as pertains to data sampling and the associated data‐processing steps is also discussed. Various aspects of the final 3D‐ΔPDF reproducibility are explicitly tested by varying the data‐processing order and included steps, and by carrying out a crystal‐to‐crystal data comparison. Situations in which the 3D‐ΔPDF is robust are identified, and caution against a few particular cases which can lead to inconsistent 3D‐ΔPDFs is noted. Although not all the approaches applied herein will be valid across all systems, and a more in‐depth analysis of some of the effects of the data‐processing steps may still needed, the methods collected herein represent the start of a more systematic discussion about data processing and corrections in this field. Data reduction and processing as related to single‐crystal diffuse scattering and 3D‐ΔPDF experiments are explored.