This work aimed to characterise water‐in‐oil‐in‐water (W/O/W) microcapsules loading Lactiplantibacillus plantarum L3 in a simulated fermentation and storage process for yoghurt, providing support for their potential application in complex fermented milk systems. The encapsulating efficiency of microencapsulated L. plantarum L3 with modified pectin was 96.79%, the aerobic plate count was 7.83 log cfu/g after simulated gastrointestinal treatment. The microencapsulated L. plantarum L3 delayed the post‐acidification of MRS medium. The cell‐free supernatant produced during the MRS storage period had a bacteriostatic effect. W/O/W microcapsules showed great prospects for application as a probiotics carrier in dairy products.