Damping-off disease due to Pythium aphanidermatum is one of the most harmful diseases of cucumber. One of the critical issues in the field of biological control is the establishment of a link between the beneficial bacteria screened in the laboratory and its industrial application. Therefore, when developing biocontrol agents, it is necessary to study the optimization of mass production conditions and to select a suitable carrier for their final formulation. In this study, an attempt was made to provide a suitable formulation for a Streptomyces fulvissimus Uts22 strain based on alginate–Arabic gum and nanoparticles (SiO2 and TiO2) with a layer-by-layer technique. X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR) studies showed that when Arabic gum was added to the composition, an electrostatic interaction occurred between alginate and Arabic gum. The scanning electron microscope image of beads show a cubic shape and good dispersion of microcapsules. The encapsulation efficiency in the prepared formulation was reported to be 94%. The maximum release of bacteria from the capsule was recorded on the 35th day of storage, about 109 CFU/gr. The greenhouse experiments showed that encapsulated bacteria resulted in a 95% reduction in damping-off disease of cucumber and showed more potential effects on increasing plant growth traits than free bacteria. This encapsulation strategy can be considered as a suitable alternative for future applications in the agricultural field.