Outbreeding confers an evolutionary advantage, and flowering plants have evolved a variety of contrivances for its maximization. However, neither fruit set nor seed set is realized to its fullest potential for a variety of reasons. The causes of low flower to fruit and seed to ovule ratios were investigated in naturally occurring bael trees (Aegle marmelos) at two sites for three seasons. The study established that the mass effect of synchronized flowering attracted a variety of insect pollinators to the generalist flowers; Apis dorsata was the most efficient pollinator. The seed to ovule ratio was low despite high natural pollination efficiency (c. 2400 pollen per stigma). Although pollination-induced structural and histochemical changes in the style allowed many (9.5 ± 2.1) pollen tubes to grow, only cross-pollen tubes could grow through the style. Gametophytic self-incompatibility, manifested in the stylar zone, resulted in a significantly slower growth rate of self-pollen tubes. The occurrence of obligate self-incompatibility, coupled with increased self-pollen deposition (geitonogamy), caused a significant number of flowers to abort. Fruit retention in the trees declined from 40% to 12% as a result of abortion of fruits at different stages of development. The number of mature fruits on a tree was negatively correlated (r = −0.82) with their size. It is inferred that low natural fecundity in A. marmelos is primarily a result of obligate self-incompatibility and strong post-fertilization maternal regulation of allocation of resources to the developing fruits. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172, 572–585.