The effect of adding trehalose in the culture medium on Lactiplantibacillus plantarum LIP-1 was investigated during spray- and freeze-drying. Although previous studies reported that the enhancement of bacterial resistance is due to intracellular trehalose accumulation, our study revealed that it was related to trehalose metabolism by the strain, and not accumulation. The underlying mechanisms were mainly related to the activation of l-glutamic acid and cysteine metabolic pathways during trehalose metabolism. First, murL, murD, and vanY in the l-glutamic acid metabolic pathway were significantly upregulated, increasing peptidoglycan synthesis and thus improving the cell wall integrity during drying process. Second, gshA in the cysteine metabolic pathway was upregulated, increasing intracellular glutathione content, enhancing antioxidant capacity, and thereby reducing the degree of cell membrane damage during drying process. Third, alkaline substances produced during l-glutamic acid and cysteine metabolisms increased the intracellular pH and reduced the degree of DNA damage caused by acid stress.