Counteracting goat reproduction seasonality and ensuring acceptable fertility rates are critical points of the success of selection of synchronisation protocols. The present study aims to investigate the factors that affect the performance of specific protocols to increase the probability of pregnancy results in the Murciano-Granadina breed within the official breeding program and way in which such factors interrelate. This study evaluated 11,008 artificial inseminations carried out between 2010 and 2013, using three different synchronisation protocols and eCG combinations. A categorical regression model (CATREG) was used to determine the impact of farm, doe age, birth number, kidding type, kid number, number of alive and dead born kids, synchronisation protocol, kidding month, type of semen, kidding season, eCG concentration, and their inter-actions. Results indicated that all variables, except for the number of alive and dead kids and semen type, significantly (p < 0.05) contributed to explaining the variability in pregnancy rates. Conclusively, rather than the role of eCG levels and artificial insemination (AI) protocol separately, Farm x eCG x AI Protocol interaction and the multifactorial influences on pregnancy rates should be considered when selecting does for insemination to maximise the outcomes of reproductive performance.