This study describes a three-year evaluation (2017–2019) of a fertility control protocol using nicarbazin (Ovistop®) to reduce the abundance of the most conflictive colonies of feral pigeon, Columba livia var. domestica, in Barcelona, Spain, as a long-term strategy based on animal welfare. The treatment was supplied to 34 pigeon colonies by automatic hopper feeders installed in public areas. A superiority study and a population monitoring study were carried out to evaluate differences in the abundance of the colonies, as well as the proportion of juveniles, the possible intake of nicarbazin by non-target species and the movement of individuals among colonies. The results showed statistical differences in the population trends between the test (−22.03%) and control (+12.86%) groups, and a significant steady decreasing trend in the pigeon abundance (−55.26%) was registered until the end of 2019. The proportion of juveniles was significatively lower in the test colonies, and a non-target species (Eurasian collared doves, Streptopelia decaocto) was observed consuming in a residual form. The protocol using nicarbazin is able to both control the abundance of pigeons, with no impact over non-target species, and respond to the public interest about animal welfare by providing an ethical method to manage overabundant and/or conflictive populations.