Bio‐compatible ionic liquids (Bio‐ILs) represent a class of solvents with peculiar properties and exhibit huge potential for their applications in different fields of chemistry. Ever since they were discovered, researchers have used bio‐ILs in diverse fields such as biomass dissolution, CO2 sequestration, and biodegradation of pesticides. This review highlights the ongoing research studies focused on elucidating the microscopic structure of bio‐ILs based on cholinium cation ([Ch]+) and amino acid ([AA]−) anions using the state‐of‐the‐art
and classical molecular dynamics (MD) simulations. The microscopic structure associated with these green ILs guides their suitability for specific applications. ILs of this class differ in the side chain of the amino acid anions, and varying the side chain significantly affects the structure of these ILs and thus helps in tuning the efficiency of biomass dissolution. This review demonstrates the central role of the side chain on the morphology of choline amino acid ([Ch][AA]) bio‐ILs. The seemingly matured field of bio‐ILs and their employment in various applications still holds significant potential, and the insights on their microscopic structure would steer the field of target specific application of these green ILs.