This study was aimed to use soy protein isolate (SPI) and high methoxy pectin (HMP) as encapsulating materials for probiotic bacterial (Lactobacillus delbrueckii) delivery systems. The encapsulation conditions were optimised, and scanning electron microscopy (SEM) was used to characterise the microstructural changes of the microcapsule. The results showed that the optimal conditions for microcapsule preparation were 90 mg mL−1 SPI and 1 mg mL−1 HMP, with a SPI/HMP ratio of 7:1 (v/v), and a L. delbrueckii suspension to SPI–HMP complex ratio of 1:1 (v/v). The viability of the probiotics in the microcapsules reaching the small intestine was 3 log CFU mL−1 higher than that of naked bacteria. SEM showed that the surface of the SPI–HMP compound microcapsules was smooth and that a large number of L. delbrueckii could be seen in cross-sections of the microcapsules.