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In this second part of a two‐part paper, we intend to demonstrate the impact of the previously proposed advanced quality control pipeline. To understand its benefit and challenge the proposed methodology in a real scenario, we chose to compare the outcome when applying it to the analysis of two patient populations with significant but highly different types of fatigue: COVID‐19 and multiple sclerosis (MS). ³¹P‐MRS was performed on a 3 T clinical MRI, in 19 COVID‐19 patients, 38 MS patients, and 40 matched healthy controls. Dynamic acquisitions using an MR‐compatible ergometer ran over a rest (40 s), exercise (2 min), and a recovery phase (6 min). Long and short T_R acquisitions were also made at rest for T₁ correction. The advanced data quality control pipeline presented in Part 1 is applied to the selected patient cohorts to investigate its impact on clinical outcomes. We first used power and sample …