Synthesis of lipid-protein conjugates is one of the significant techniques in drug delivery systems of proteins; however, the intact conjugation of a lipid and protein is yet challenging due to the hydrophobicity of lipid molecules. In order to facilitate easy handling of the lipid moiety in conjugation, we have focused on a microbial transglutaminase (MTG) that can ligate specific lysine (K) and glutamine (Q) residues in lipopeptides and a protein of interest. As MTG substrates, monolipid- and dilipid-fused amphiphilic short lipopeptide substrates (lipid-G3S-RHK or lipid2-KG3S-RHK) were designed. These amphiphilic lipopeptides and a model protein (enhanced green fluorescent protein, EGFP) fused with LLQG (LQ-EGFP) were both water-soluble, and thus lipid-protein conjugates were efficiently obtained through the MTG reaction with a >80% conversion rate of LQ-EGFP even using cholesterol-G3S-RHK. In vitro cell adhesion and in vivo half-life stability of the successfully obtained lipid-protein conjugates were evaluated, showing that the monocholesterol-G3S-RHK modification of a protein gave the highest cell adhesion efficiency and longest half-life time by formation of a stable albumin/lipid-protein complex.