El Niño-Southern Oscillation (ENSO) flavors have been defined to characterize ENSO events and their teleconnections. Studying El Niño flavor evolution during the Holocene period can provide valuable insights into changes over long time scales. We investigated ENSO flavor evolution using simulations spanning the last 6,000 years and present-day observations. Two approaches to computing ENSO flavors, in agreement in the present, lead to opposite trends in the last 6,000 years. The methods also differ significantly in their representation of ENSO flavor patterns. However, incorporating the sensitivity of the methods to calibration periods and mean state changes yields similar interpretations of ENSO variability changes. Both methods suggest an increase in El Niño variability spreading to the west and east tropical Pacific over the past 6,000 years. Standardizing El Niño flavor definitions is necessary for meaningful comparisons between studies and robust climate variability analysis.