Circadian clock regulates plant development and physiology by anticipating daily environmental changes. Here we studied the core clock protein involved in β-aminobutyric acid (BABA)-inducible systemic acquired resistance (SAR) resistance to Rhizopus stolonifer in peach fruit. BABA elicitation barely primed the accumulation of jasmonate or ethylene, whose regulation was associated with morning-loop gene expression. Notably, BABA-induced resistance depended on the upregulation of salicylic acid (SA) signalling, accompanied by increased transcription of specific evening-loop genes. Through Y2H screening, pull-down and co-IP analyses, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), a morning-expressed clock protein repressed by BABA, was identified as an interacting partner of NPR1 in regulating SA-dependent SAR. A CUT&Tag analysis indicated that the association of CCA1 with its target genes, which are enriched in EE or CBS motifs, was involved in SA pathway. Furthermore, EMSA, DLR, Y3H and Co-ip assays suggested that CCA1 did not directly affect the expression of SA-inducible genes but instead hindered the interaction between NPR1 and TGA1. Overexpression of PpCCA1 attenuated the transcription of SA-responsive PR genes, while mutation of PpCCA1 elevated these expressions. Collectively, PpCCA1 functions as a negative regulator of NPR1-dependent SA signalling through antagonistic crosstalk with the NPR1-TGA1 system, but BABA activates SAR by suppressing PpCCA1 in peach fruit.