Although significant progress has been made into better understanding interactions between biodiversity and wind farms, providing accurate and reliable assessment methods that allow studying the real effects of these projects is of major importance. Focusing on the Portuguese wind energy development current status and by referring to other international guidelines, the currently applied general procedures were compiled in a step-by-step process, from pre-project development to the operation phases. Today, legislation stipulates that impact assessment is mandatory for most of the energy development projects in Portugal, including wind energy. Wind farm impact assessment starts—in most cases—with baseline studies to allow prediction of the main impacts expected on wildlife, as well as the presence of endangered species and/or landscape features. This may lead to the need for layout adjustment or the definition of mitigation measures on site. When a project is approved, even if it is assumed that the major impacts have been identified and mitigated, that does not mean that it is free of negative effects. It is of major importance that the real impacts are evaluated during construction and operation phases based on the methods applied during pre-construction. In addition, the establishment of a reference area to compare with the wind farm situation is fundamental. These temporal and spatial features should be assessed by a before-after-control-impact design. A basis of the sampling and data collection methods is also addressed in this chapter according to most commonly targeted biodiversity (fauna and flora). Techniques vary from standard field surveys by one or more observers to the use of less common and more recent technologies.