Economic evaluations have been increasingly conducted in different countries to aid national decision-making bodies in resource allocation problems based on current and prospective evidence on costs and effects data for a set of competing health care interventions. In 2016, the Dutch National Health Care Institute issued new guidelines that aggregated and updated previous recommendations on key elements for conducting economic evaluation. However, the impact on standard practice after the introduction of the guidelines in terms of design, methodology and reporting choices, is still uncertain. To assess this impact, we examine and compare key analysis components of economic evaluations conducted in the Netherlands before (2010–2015) and after (2016–2020) the introduction of the recent guidelines. We specifically focus on two aspects of the analysis that are crucial in determining the plausibility of the results: statistical methodology and missing data handling. Our review shows how, over the last period, many components of economic evaluations have changed in accordance with the new recommendations towards more transparent and advanced analytic approaches. However, potential limitations are identified in terms of the use of less advanced statistical software together with rarely satisfactory information to support the choice of missing data methods, especially in sensitivity analysis.