A novel soybean flour (SBF) cell protection mechanism was successfully revealed. SBF is a new freeze-dried B. subtilis SB-MYP-1 cell (FDBSC) protective agent. SBF effectively maintained the highest survival of FDBSCs (>107 CFU/g). SBF could preserve the cell wall and membrane fluidity of FDBSCs. pgsB gene of FDBSCs with SBF was still expressed.