This work estimated the biochemical nature of the enzymatic chitosan hydrolysate (CH) as oligomeric chitooligosaccharide products resulting from microwave-aided cellulase hydrolysis of chitosan from shrimp and crab as well as their biological effects and potential preservative application. The microwave irradiation was conducted at 125 W for 15 min simultaneously during the cellulase degradation of shrimp and crab chitosan, previously prepared by a 30-min microwave-aided deacetylation (86.7% and 82.7% degree of deacetylation), producing shrimp chitosan hydrolysate (SCH) and crab chitosan hydrolysate (CCH), respectively. The products SCH and CCH were tested for their solubility in distilled water, viscosity, molecular weight (Mw), FTIR, mass spectra, antioxidant, and antibacterial activities. The obtained SCH and CCH were incorporated into two food systems (yogurt and orange juice) at proportions of 0.08–0.12 g/100 mL as potential preservatives. The average Mw of SCH and CCH was 14.79 and 13.18 kDa, respectively, coupled in each case with 1–6° of polymerization (DP), strong antibacterial and antioxidant activities, and the capacity to dissolve in water in all proportions, becoming more soluble as weight decreased. The chemical, microbiological, and sensory changes in orange juice and yogurt were investigated at 0, 15, and 30 days of cold storage after being enriched with these ingredients. Over the 30-day storage period, the orange juice and yogurt showed enhanced physicochemical, microbiological, and sensory characteristics based on the content of chitosan hydrolysate. The study provided potentially a new and safe preservation technology for food systems.