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Abstract We describe how typical relative humidity (RH) profiles change systematically through the phases of the Madden–Julian Oscillation (MJO). We use 18 years of classified RH‐profiles from the Atmospheric Infrared Sounder, clustered without prior knowledge of large‐scale dynamics or occurrence‐region. Occurrence probability (OP) anomalies of RH‐profiles classes exhibit classical MJO patterns: Large positive OP anomalies of the RH‐profile class with most moisture in the free troposphere are co‐located with the largest positive precipitation anomalies. About 10 days prior to this deep convective core large OP anomalies of a RH‐profile class occur consistent with lower atmospheric moistening, supporting a ubiquitous role of pre‐moistening in MJO propagation. Since each RH‐profile class is associated with distinct dynamics (most of which are subgrid‐scale to climate models) our results can serve as process‐based diagnostics to investigate parameterization shortcomings of climate models preventing them to simulate the MJO accurately.