<p>Risen temperatures result in a notable decline in pepper yield, predominantly due to their direct impact on fruit set. The female gametophyte has been less studied than male reproductive organs but proven to be heat-sensitive. Phytohormones regulate responses to adverse environmental conditions and developmental processes as fruit set, but there is lack of research on pepper reproductive organs. Grafting has emerged as a promising strategy to alleviate the consequences of heat stress, as reported by our previous work. The objectives were to examine the effect of heat stress on the hormonal balance of the pepper ovary (IAA, ACC, ABA, GAs, CKs, SA and JA) during early fruit set (prior to four days post-anthesis) and to evaluate the influence of pepper rootstock genotypes to enhance fruit set and reduce the impact of heat stress. The hormonal quantification across flower stages highlights the complexity of the mechanisms by which hormones influence fruit development. Heat stress decreased IAA, ZR, GA1, ABA, JA and SA content in the pepper ovary and increased tZ, iP and ACC levels. Rootstocks modulated ACC, iP, ABA, JA, GA1 and GA4 content in the variety under heat stress. Variety grafted onto A57 (VA/A57) reduced fruit set and seed number losses under heat stress compared with VA/A55, VA/VA and VA, associated with a better ability to cope with heat stress in the grafted variety.</p>