The squaric acid mediated bioconjugation reaction is an attractive approach for the amine-selective protein modification with side-chain functional polymers. This manuscript presents 3 squaric acid based atom transfer radical polymerization (ATRP) initiators that significantly expand the scope of this bioconjugation reaction to a broad range of synthetic polymers that can be prepared by ATRP. Two proof-of-principle studies are discussed that demonstrate the feasibility of these novel initiators for the preparation of protein-synthetic polymer conjugates via both the grafting-onto as well as the grafting-from strategy. ATRP of polyethylene glycol methacrylate (PEGMA) with these initiators was used to generate a library of linear, mid-functional and 3-arm squaric acid functionalized PPEGMA derivatives. These PPEGMA polymers could subsequently be grafted onto bovine serum albumin (BSA), which was selected as a model protein. Alternatively, BSA could also be modified with these squaric acid based initiators to afford protein macroinitiators, which were successfully used to mediate ATRP of PEGMA and generate BSAPPEGMA conjugates in a grafting-from process.