The available methodologies to estimate the obesity-attributable mortality fraction (OAMF) affect the levels found and hamper the construction of time series. Our aim was to assess the impact of using different techniques to estimate the levels and the trends in obesity-attributable mortality for The Netherlands between 1981 to 2013. Using Body Mass Index (BMI), all-cause and cause-specific mortality data, and worldwide and European relative risks (RRs), we estimated OAMFs using three all-cause approaches (partially adjusted, weighted sum, and the two combined) and one cause-of-death approach (Comparative Risk Assessment; CRA). We adjusted the CRA approach to purely capture obesity (BMI ≥ 30 kg/m2). The different approaches led to a range of estimates. The weighted sum method using worldwide RRs generated the lowest (0.9%) while the adjusted CRA approach using 2013 RRs generated the highest estimate (1.5%). Using European-specific RRs instead of worldwide RRs resulted in higher estimates. Most of the approaches revealed an increasing OAMF over the period 1981 to 2013 especially from 1993 onwards except for the adjusted CRA approach among women. Estimates of OAMF levels and trends differed depending on the method applied. Given the limited available data, we recommend using the weighted-sum method to compare obesity-attributable mortality across European countries over time.