The aims of this study were to obtain chitooligosaccharides (COS) from chitosan (CH) with improved functional properties and comparison of the use of two different enzymes: commercial cellulase (CL) and the dedicated enzyme chitosanase (CS). After enzymatic reaction, chitosan oligomers (NFs) were isolated by methanol into two fractions: precipitate (HMF) and supernatant (LMF). The occurrence of a hydrolysis reaction was confirmed by an increased reducing sugar content and viscosity reduction of chitosan oligomers. CPMAS 13C NMR analysis confirmed the dissimilar cleavage mechanism of the enzymes used. LMF and NF fractions were characterised by improved solubility in water (94.56%) compared to the HMF and CH samples (70.64%). Thermogravimetric analysis (TGA) showed that the HMF decomposed in two-stage process while CH, NF, and LMF decomposed in a three-stage process. The greatest mass loss of LMF samples (58.35%) suggests their sensitivity to high-temperature treatments. COS were a mixture of DP (degrees of polymerisation) from 3 to 18 hetero-chitooligomers, with an average Mw of <3 kDa. CL consisted of more low-DP products (DP 3–7) than COS made with CS. LMF characterised by DP~2 showed lower DPPH radical scavenging activity than HMF and NF with DP 3–7. The ability to reduce Escherichia coli increased in the given order: LMF > NF > HMF > CH.