The utilization of ionic liquids (ILs) in metal extraction has been massively studied due to their excellent extraction ability, vast structural tunability, and low volatility. However, several ILs can be severely toxic, depending on the structure. It is significant to extract metal ions in a greener way for sustainability, yet the development of low-toxicity ILs for metal extraction remains a challenge. We prepared a series of potentially biocompatible ILs composed of amino acid ester (AAE)-based cations, with varying alkyl chain lengths and amino acid types and a fixed linoleate anion. An in vitro cytotoxicity study on HeLa cells indicates that the EC50 value of the synthesized ILs was ca. 2 orders of magnitude higher than that of commercial ILs (Aliquat 336 and Cyphos 104), suggestive of the low toxicity of the newly synthesized ILs. The ILs extracted the transition metals in the following order: Ni2+ > Co2+ > Mn2+. The separation factors for Ni/Co and Co/Mn ranged from 0.8 to 55 and from 0.6 to 50, respectively. In addition, l-leucine butyl linoleate exhibited highly selective extraction toward Au3+ and Pd2+ over Pt4+ with separation factors for Au/Pt and Pd/Pt of 37 and 40 in 0.05 mol/L HCl, respectively. Thus, AAE-based ILs are promising biocompatible extractants for metals.