Plant MIR genes are independent transcription units that encode long primary miRNA precursors, which usually contain introns. For two miRNA genes, MIR163 and MIR161 , we show that introns are crucial for the accumulation of proper levels of mature miRNA. Removal of the intron in both cases led to a drop‐off in the level of mature miRNAs. We demonstrate that the stimulating effects of the intron mostly reside in the 5′ss rather than on a genuine splicing event. Our findings are biologically significant as the presence of functional splice sites in the MIR163 gene appears mandatory for pathogen‐triggered accumulation of miR163 and proper regulation of at least one of its targets.