Arabinoxylans (AX) and protease treated AX (AXP) were subjected to enzymatic hydrolysis with endoxylanase and arabinofuranosidase to obtain hydrolyzed AX (HAX) and AXP (HAXP), whose ability to promote Bifidobacterium infantis and Bifidobacterium longum growth was investigated. Further, the effect of cross-linked AX on the growth of bifidobacteria was also explored. Bifidobacteria showed the highest growth on AX and AXP, while HAX and HAXP did not have a significant impact on bacterial growth. The laccase cross-linking of AX stimulated the growth of bifidobacteria, possibly due to its gel-like structure which favored the bacteria-substrate (AX) interaction. The laccase-induced cross-linked AX (AXG) and alginate (SA) were used to prepare encapsulating matrices. The ability of AXG-SA matrices to encapsulate and protect probiotic bacteria (Lactobacillus rhamnosus GG, Streptococcus thermophilus and B. longum) viability under storage conditions was investigated. The AXG matrices presented the highest encapsulation efficiencies (55–77%) for all three strains, when AXG-SA and SA matrices were compared. Significantly higher levels (∼7 logs) of L. rhamnosus GG were recovered from AXG and AXG-SA matrices after 28 days of storage under aerobic conditions at 4 °C compared to SA matrices (∼4 logs). The results indicated that the incorporation of AX into the matrices played a significant role on the survival of encapsulated bacteria during storage, which could be attributed to the stability of the covalent cross-linked network formed during AX gelation that protected bacterial viability. Thus, the matrices based on AXG could be promising materials to encapsulate and protect probiotic bacteria for targeted-delivery to the colon.