Alternative splicing (AS) of pre-mRNAs is an important gene regulatory mechanism shaping the transcriptome. AtMC1 is an Arabidopsis thaliana type I metacaspase that positively regulates hypersensitive response (HR). Here, we found that AtMC1 is a negative regulator of plant immunity to the bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 and is physically associated with Sm-like4 (LSM4), which is involved in pre-mRNA splicing. AtMC1 and LSM4 protein levels both increased with their co-expression as compared with their separate expression in vivo. Like AtMC1, LSM4 negatively regulates plant immunity to Pst DC3000 infection. By RNA-seq, AtMC1 was shown to modulate the splicing of many pre-mRNAs including 4CL3, which is a negative regulator of plant immunity. Moreover, atmc1 mutant plants accumulated microRNAs (miRNAs) such as miR398b, miR399a, miR165a and miR159a at a low level than wild-type Arabidopsis Col-0 plants. Furthermore, AtMC1 affected pri-miRNA processing. RNA immunoprecipitation revealed that AtMC1 interacted with these pri-miRNAs in vivo, suggesting that AtMC1 might suppress their processing by directly binding to them. In addition, we found that MC1-mediated plant immunity is conserved in tomato. Thus, AtMC1 plays a regulatory role in both miRNA expression and pre-mRNA splicing, which might contribute to AtMC1-mediated plant immunity.