In recent decades, the integration of horses in European rewilding initiatives has gained widespread popularity, driven by their potential for regulating vegetation and restoring natural ecosystems. However, employing horses in conservation efforts presents some important challenges, which we here explore and discuss. These challenges encompass the strong and long-lasting emotional bond to horses, the mostly overlooked issues of low genetic diversity and high susceptibility to hereditary diseases in selected animals, as well as the insufficient consideration for the social behaviour of horses in natural populations. In addition, management of free-roaming horses involves intricate welfare, ethics and legislative dimensions, whereby anthropocentric population control initiatives may be detrimental to horse group structures, and individual welfare tends to be prioritised over the health of populations and even ecosystems. We provide comprehensive recommendations to overcome these challenges, and advocate for intensified collaboration between conservation biologists and practitioners, enhanced communication with the general public, and decision-making informed by a thorough understanding of the genetic makeup, common pathological conditions and social behaviour of the animals.