GENERAL CONTROL NONDEREPRESSIBLE 5 (GCN5) is a histone acetyltransferase in Arabidopsis thaliana involved in numerous biological processes, including flower development. Previous studies have demonstrated GCN5's interaction with the CLAVATA (CLV) pathway, influencing gynoecium development potentially through modulating auxin and cytokinin dynamics and regulating WUSCHEL (WUS) expression. In clv1gcn5 double mutants, noticeable phenotypic alterations include reduced or absent valves, an enlarged stigma, and an elongated gynophore, indicative of disruptions in both apical-basal and mediolateral axes of the gynoecium. SPATULA (SPT), a bHLH transcription factor, is a pivotal regulator in gynoecium development. Intriguingly, this work demonstrates that SPT mutations partially alleviate clv1gcn5 phenotypes; specifically, they restore the formation of valves in the ovary. Transcriptomic analysis of gynoecium mutants, including spt, clv1, gcn5 and the various genetic combinations, reveals their significant impact on apical-basal, mediolateral, and adaxial-abaxial polarity axes. Genes such as STY1/2, PID, and TCP15 governing apical-basal polarity were misexpressed in clv1gcn5 mutants and showed either complete or partial restoration of their levels in sptclv1gcn5 gynoecia. Similarly, mediolateral genes, including CUC2, FIL, YAB3, and JAG, downregulated in clv1gcn5, were reinstated in sptclv1gcn5 mutants. Notably, adaxial-abaxial factors like REV, ATHB4, and AS1 follow a similar pattern, suggesting that GCN5, CLV1 and SPT are essential players in the proper determination of polarity axes in the Arabidopsis gynoecium. This study unveils the intricate interplay among GCN5, CLV1, and SPT, underscoring their pivotal roles in orchestrating gene expression and polarity determination during Arabidopsis thaliana gynoecium development.