Acca sellowiana (Berg) Burret is a predominantly allogamous species with hermaphrodite flowers that has barriers to self-fertilisation such as dichogamy by protogyny and self-incompatibility. This study aimed to identify when self-incompatibility occurs in A. sellowiana flowers submitted to self-pollinations. Pollinations were made using nine known self-incompatible accessions in several treatments including manual cross-pollination, manual self-pollination, no pollination and natural pollination. Flowers were pollinated and pistils collected at times ranging from 1 to 30 days after pollination (DAP). In both cross- and self-pollinations the fertilisation occurred from 18 DAP and the zygote was visualised at 24 and 26 DAP, respectively. The abscission of the self-pollinated flowers increased from 26 DAP onwards, when significant differences (P < 0.05) were found for the percentage of abscission among self-pollinated and cross-pollinated flowers. At 30 DAP, 72% of self-pollinated flowers were abscised. The size of ovules and ovaries of self-pollinated flowers showed no significant difference from those of non-pollinated flowers throughout 30 DAP, while those from cross-pollinated flowers were significantly larger (P < 0.05) than the other treatments from 22 and 24 DAP, respectively. After 40 DAP, there was no fruit development in self-pollination and non-pollination treatments. Our study brings greater clarity to the mechanism of self-incompatibility in A. sellowiana, indicating late-acting self-incompatibility occurring through the rejection/abscission of self-pollinated flowers precisely after syngamy and zygote formation.