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<i>Morganella morganii</i>, a spoilage bacterium in fermented foods, produces harmful biogenic amines (BAs). Although <i>Lactiplantibacillus plantarum</i> is widely used to inhibit spoilage bacteria, the inhibition pattern and inhibition mechanism of <i>M. morganii</i> by <i>Lpb. plantarum</i> are not well studied. In this study, we analysed the effects of the addition of <i>Lpb. plantarum</i> cell-free supernatant (CFS) on the growth and BA accumulation of <i>M. morganii</i> and revealed the mechanisms of changes in different BAs by using RNA sequencing transcriptome analysis. The results showed that <i>Lpb. plantarum</i> CFS could significantly inhibit <i>M. morganii</i> BAs in a weak acid environment (pH 6), and the main changes were related to metabolism. Carbohydrate and energy metabolism were significantly down-regulated, indicating that <i>Lpb. plantarum</i> CFS inhibited the growth activity and decreased the BA content of <i>M. morganii</i>. In addition, the change in histamine content is also related to the metabolism of its precursor amino acids, the change in putrescine content may also be related to the decrease in precursor amino acid synthesis and amino acid transporter, and the decrease in cadaverine content may also be related to the decrease in the cadaverine transporter. The results of this study help to inhibit the accumulation of harmful metabolites in fermented foods.