This study seeks the optimal method for recovering loaded bacteria from filtering facepiece respirators (FFRs) and investigates the effects of artificial saliva (AS), artificial perspiration (AP) and storage conditions on the survival of bioaerosols and the filter performance of FFRs. Bioaerosols were generated using a Collison nebulizer in a test system and loaded on either N95 or surgical masks. Elution using centrifuge at 3500 rpm for ten min followed by vortexing for one min yielded a high relative survival (RS) rate of airborne Bacillus subtilis (BS) spores. When AS was added to the N95 FFR, the RS of BS declined during the first eight hours of storage and then increased to reach its highest value after 24 hr of storage. The worst case with the highest RS was at 37°C and 95% RH (p < 0.001). When AP was added to the N95 FFR and stored under the worst conditions, RS increased by over 100% during eight hours of storage. When AS was added to a surgical mask, the RS also increased by over 100% in eight hours of storage, but when AP was added to the surgical mask, RS immediately declined. When Escherichia coli (EC) were tested, their RS was lower than those of the BS samples. (Following loading with bacteria, the particle penetration and filter quality factor (qf) increased (p < 0.001) but the slope of the linear regression between the pressure drop (∆p) and the flow rate through the filter was not statistically significantly changed (p = 0.233). In conclusion, AS and AP increased the survival of BS; AP was especially effective in N95 masks and AS was especially effective in surgical masks.