Drying of probiotic cultures is the main form of stabilization but dry probiotics face oxidative stress. The addition of antioxidants has been employed for protection of probiotics against oxidative stress, but results on the addition of antioxidants remain inconclusive. In this work, matrices of whey protein isolate fibrils (WPIF) with epigallocatechin gallate (EGCG) or glutathione (GSH) were used. Probiotic viability during ambient storage decreased in the order of WPIF > WPIF + EGCG > WPIF + GSH > WPI > WPI + EGCG > WPI + GSH. The improved protection of WPIF might be explained by its better cell encapsulation and the high antioxidant activity of WPIF. Both antioxidants accelerated the death of probiotic, which might be related with the antimicrobial activity or the cytotoxicity of the reaction products. This study proposed an excellent wall material of amyloid fibrils for probiotic protection during ambient storage, and questioned the "common sense" that antioxidants protect probiotics from oxidative stress.