Using O-SP–core (O-SPcNH2) polysaccharide, isolated from Vibrio cholerae O1 lipopolysaccharide (LPS) and related synthetic substances, a detailed study of factors that affect conjugation of bacterial polysaccharides to protein carriers by squaric acid chemistry to form conjugate vaccines has been carried out. Several processes previously unrecognized, which take place during the squarate labelling of the O-SPcNH2 and subsequent conjugation of the squarate (O-SPcNH–SqOMe) formed, have been identified. The efficiency of conjugation at pH 8.5, 9.0, and 9.5 to each of bovine serum albumin (BSA) and the recombinant tetanus toxin fragment C (rTT-Hc) has been determined. The study led to a protocol for more efficient labeling of O-SPcNH2 antigen with the methyl squarate group, to yield a higher quality, more potent squarate conjugation reagent. Its use resulted in about two-fold increase of conjugation efficiency (from 23–26% on BSA to 51% on BSA and 55% on rTT-Hc). The spent conjugation reagent could be recovered and regenerated by treatment with MeI in the absence of additional base. The immunological properties of the experimental vaccine made from the regenerated conjugation reagent were comparable to those of the immunogen made from the parent O-SPcNH–SqOMe.