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ABSTRACT Earthquake stress drop—a key parameter for describing the energetics of earthquake rupture—can be estimated in several different, but theoretically equivalent, ways. However, independent estimates for the same earthquakes sometimes differ significantly. We find that earthquake source complexity plays a significant role in why theoretically (for simple rupture models) equivalent methods produce different estimates. We apply time- and frequency-domain methods to estimate stress drops for real earthquakes in the SCARDEC (Seismic source ChAracteristics Retrieved from DEConvolving teleseismic body waves, Vallée and Douet, 2016) source time function (STF) database and analyze how rupture complexity drives stress-drop estimate discrepancies. Specifically, we identify two complexity metrics—Brune relative energy (BRE) and spectral decay—that parameterize an earthquake’s complexity relative to the standard Brune model and strongly correlate with the estimate discrepancies. We find that the observed systematic magnitude–stress-drop trends may reflect underlying changes in STF complexity, not necessarily trends in actual stress drop. Both the decay and BRE parameters vary systematically with magnitude, but whether this magnitude–complexity relationship is real remains unresolved.