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The development of high-performance and environmentally-compatible lubricants is crucial for minimizing energy losses in mechanical systems and increasing the lifetime of moving mechanical components, thus preserving our environment. While ionic liquids (ILs) have emerged as promising next-generation materials for lubrication purposes owing to their attractive physico-chemical properties, several challenges currently limit their use in engineering applications, including their high cost and corrosivity. Recently, eco-friendly, protic ILs (PILs) have been synthesized and showed great advantages compared to tradition (aprotic) ILs, such as low cost, ease of preparation, and good lubricating properties. Despite these advancements, remarkably little is known about the interrelationship between PIL molecular structure and lubrication mechanisms. In this work, the physico-chemical and lubricating properties of a family of PILs synthesized by using only renewable, biodegradable, and biocompatible products and constituted by the same choline cation and amino-acid anions with different side chains, were investigated. The molecular structures of the choline amino acid-based ionic liquids (AAILs) were confirmed through magnetic resonance and Fourier transform infrared spectroscopy, while their thermal behavior was evaluated by differential scanning calorimetry and thermogravimetric analysis. The antiwear and friction-reducing performance of the choline AAILs when used as neat lubricants was studied as a function of normal load by reciprocating ball-on-flat tribometry using steel-steel contact. Surface analytical measurements (Raman and XPS) performed on the worn steel surfaces confirmed that the excellent lubricating performance of choline AAILs originates from the formation of oxygen- and carbon-rich tribolayers. The formation of these protective layers are influenced by the applied normal load and the molecular structure of the amino acid. The results of this work open the path for the rational design of environmentally-friendly PILs for tribological applications.