Poor seed set is a limiting factor in alfalfa breeding, as it slows the selection response. One strategy used to overcome this problem is to search for mutations of inflorescence morphology. Long-peduncle (lp), branched-raceme (br) and top-flowering (tf) inflorescence mutations increase the number of flowers per inflorescence, but they do not improve seed set per flower. Here we assessed pollen tube growth in styles of those inflorescence mutants and we observed embryo and endosperm development in seeds 1 to 16 days after pollination (DAP). The number of pollen tubes penetrating the style and the ovary was similar in all tested mutants and in the reference cultivar Radius. At 2 DAP, fertilized ovules were 2.7–3.9 times less numerous in certain inflorescence mutants than in the short-raceme cv. Radius. Ovule degeneration progressed at 2–4 DAP in all analyzed plants. Most ovules were not properly developed in the control cultivar (62%), nor in the forms with mutated inflorescence morphology (69–86%). The number of seeds per pod was lowest in the tf form despite its having the highest number of ovules per ovary. It appears that the number of ovules per pistil is not a crucial factor in seed set in alfalfa when fertilization efficiency is very low. Both poor fertilization and gradual ovule degeneration were factors causing poor seed set in the investigated alfalfa genotypes.