Dairy cattle breeding has historically focused on relatively small numbers of elite bulls as sires of sons. In recent years, even if generation intervals were reduced and more diverse sires of sons could have been selected, genomic selection has not fundamentally changed the fact that a large number of individuals are being analyzed. However, a relatively small number of elite bulls are still siring those animals. Therefore inbreeding-derived negative consequences in the gene pool have brought concern. The detrimental effects of non-additive genetic changes such as inbreeding depression and dominance have been widely disseminated while seriously affecting bioeconomically important parameters because of an antagonistic relationship between dairy production and reproductive traits. Therefore, the estimation of benefits and limitations of inbreeding and variance of the selection response deserves to be evaluated and discussed to preserve genetic variability, a significant concern in the selection of individuals for reproduction and production. Short-term strategies for genetic merit improvement through modern breeding programs have severely lowered high-producing dairy cattle fertility potential. Since the current selection programs potentially increase long-term costs, genetic diversity has decreased globally as a consequence. Therefore, a greater understanding of the potential that selection programs have for supporting long-term genetic sustainability and genetic diversity among dairy cattle populations should be prioritized in managing farm profitability. The present review provides a broad approach to current inbreeding-derived problems, identifying critical points to be solved and possible alternative strategies to control selection against homozygous haplotypes while maintaining sustained selection pressure. Moreover, this manuscript explores future perspectives, emphasizing theoretical applications and critical points, and strategies to avoid the adverse effects of inbreeding in dairy cattle. Finally, this review provides an overview of challenges that will soon require multidisciplinary approaches to managing dairy cattle populations, intending to combine increases in productive trait phenotypes with improvements in reproductive, health, welfare, linear conformation, and adaptability traits into the foreseeable future.