Bacterial resistance to chemical and physical methods in food processing, and the consumers’ demand for food free of chemical additives challenge the food industry to identify new approaches for food preservation. Affordable and novel antimicrobial compounds from food derived sources are an interesting field of research. This study investigated antimicrobial compounds derived from glucosamine or from glucosamine and fish gelatin peptides. Reaction of glucosamine in aqueous solution at 50 °C in the presence and absence of iron produced the five α-dicarbonyl compounds glucosone, 3-deoxyglucosone, glyoxal, methylglyoxal and diacetyl. The reaction was followed up to 48 h of incubation by UV/Vis absorbance profiles and pH variations, in order to understand where the major changes occurred during the progress of the reaction. Major changes in UV/Vis profiles were found after 3 h and 48 h of incubation. The reaction mixture exhibited antimicrobial activity at 5% (w/v) against Escherichia coli AW 1.7 and this activity was partially attributable to the α-dicarbonyls. Furthermore, fish gelatin peptides were modified by chemical glycation or enzymatic glycosylation with glucosamine at room temperature; the five α-dicarbonyls glucosone, 3-deoxyglucosone, glyoxal, methylglyoxal and diacetyl were also found in the conjugated mixtures. The conjugated samples of fish gelatin peptides with glucosamine were fractionated by lectin affinity and reverse phase liquid chromatography. The resultant fractions of glycopeptides reduced the growth of E.coli AW 1.7 at lower concentration of 1% (w/v) compared with the original conjugates. In this study, antimicrobial compounds such as α-dicarbonyls and glycopeptides were separated and identified after glucosamine autocondensation and glucosamine-fish gelatin peptides conjugation. The potential antimicrobial activity exhibited by glucosamine and glucosamine-peptides suggests that it is feasible to use glucosamine as a functional food ingredient that might serve for food preservation.