The impact of the operation of wind farms on birds and bats in terms of true fatality is still unknown. However, fatality numbers can be estimated using statistical methods that have improved over recent years, aiming to provide a closer representation of the real ecological conditions. To assess which statistical methods have been used to estimate bird and bat fatality in the Portuguese context, we analysed 225 wind farm fatality monitoring reports, published between 2005 and 2015, and concluded that the methodology is not standardised. Importantly, the estimators used to calculate fatality differ amongst the environmental specialists and over time. These findings can hamper an integrated analysis of the impacts caused by wind farms at a national scale and bias the importance of cumulative impacts. We also reviewed the most recently published fatality estimators in order to better understand their applicability to the Portuguese private environmental consultancy context. Our analysis identified the criteria that most influences the implementation of a valuable fatality estimation methodology and assembled a list of considerations that a best practice guidelines protocol can be based upon for application at both the regional and national scale.