Abstract This paper aims to provide empirical researchers with an overview of the methodological issues that arise when estimating total factor productivity at the establishment level, as well as of the existing (parametric and semi‐parametric) techniques designed to overcome them. Apart from the well‐known simultaneity and selection bias, attention is given to methodological issues that have emerged more recently and that are related to the use of deflated values of inputs and outputs (as opposed to quantities) in estimating productivity at the firm level, as well as to the endogeneity of product choice. In discussing the estimation procedures applied in the literature, attention is given to recent developments in the field. Using data on single‐product firms active in the Belgian food and beverages sector, the most commonly applied estimators are illustrated, allowing for comparison of the obtained productivity estimates by way of a simple evaluation exercise.