In the present study, phenotypic correlations and direct and indirect effects were estimated in a breeding population of cacao involving 22 full-sib families from 14 reciprocals and 8 direct crosses to obtain information aiming to increase selection efficiency for higher production. Path analysis was used to obtain estimates at the family level, within families, and the individual level. High phenotypic correlation coefficients were found between the total number of pods per tree and frosty pod rot incidence, with bean dry weight per tree, at the family (r = 0.91 and − 0.84, p < 0.001) and individual levels (r = 0.89 and − 0.50, p < 0.001), respectively. Path analysis revealed that the total number of pods per tree had the highest positive direct effects (0.66 to 1.05) on bean dry weight per tree expression. Likewise, indirect effects via the total number of pods per tree were important to explain the significant association of the other variables with the bean dry weight yield per tree. Variations in the correlation significance and direct and indirect effect magnitudes were observed among sample size, families, reciprocal and direct crosses, years, and bimonthly. However, beyond the influence of these, the total number of pods per tree had the greatest effects on production. These results suggest that indirect selection on the total number of pods per tree would improve selection efficiency for high bean yield in these breeding populations, accelerating and reducing costs than using a larger number of traits. The low heritability associated with the number of pods per tree might be beneficial in the second step of the selection process, considering other yield components of higher heritability as bean dry weight per pod. Also, extrapolation of the results should be done with care, considering that genetic parameter estimates are strictly valid for the population and environment studied, especially here that the number of parents used is a small sample (although important) of the parents used in cacao breeding programs.