Summary Poly(A) tail shortening is a critical step in messenger RNA (mRNA) decay and control of gene expression. The carbon catabolite repressor 4 (CCR4)‐associated factor 1 (CAF1) component of the CCR4‐NOT deadenylase complex plays an essential role in mRNA deadenylation in most eukaryotes. However, while CAF1 has been extensively investigated in yeast and animals, its role in plants remains largely unknown. Here, we show that the Citrus sinensis CAF1 (CsCAF1) is a magnesium‐dependent deadenylase implicated in resistance against the citrus canker bacteria Xanthomonas citri . CsCAF1 interacted with proteins of the CCR4‐NOT complex, including CsVIP2, a NOT2 homologue, translin‐associated factor X (CsTRAX) and the poly(A)‐binding proteins CsPABPN and CsPABPC. CsCAF1 also interacted with PthA4, the main X. citri effector required for citrus canker elicitation. We also present evidence suggesting that PthA4 inhibits CsCAF1 deadenylase activity in vitro and stabilizes the mRNA encoded by the citrus canker susceptibility gene CsLOB1 , which is transcriptionally activated by PthA4 during canker formation. Moreover, we show that an inhibitor of CsCAF1 deadenylase activity significantly enhanced canker development, despite causing a reduction in PthA4‐dependent CsLOB1 transcription. These results thus link CsCAF1 with canker development and PthA4‐dependent transcription in citrus plants.