On aqueous two-phase systems (ATPS) composed of ionic liquids (ILs) it is often observed that the increase in the cation alkyl side chain length enhances the biomolecules extraction for the IL-rich phase. However, mounting evidences suggest that very long alkyl side chains are unfavorable to the separation. This change on the extraction trends was previously suggested to be due to micelle formation; yet, no evidence was provided and an evaluation of the effect of the pH and of the hydrophobicity of the biomolecules on the partition coefficients for a homologous family of ILs was never carried out. In this work a systematic study of the cation alkyl side chain length effect on the partitioning of a series of alkaloids of variable hydrophobicity in ATPS constituted by 1-alkyl-3-methylimidazolium chloride ILs ([Cnmim]Cl) and potassium citrate (at controlled pH) was conducted. The results here reported show that the alkaloids partition coefficients increase with the cation alkyl chain length until the formation of micelles on the systems with cations larger than [C6mim]Cl. Cations with longer aliphatic chains are not favorable for the extraction of alkaloids, inducing a trendshift on the system by decreasing the partition coefficients or the preferential migration for the IL-rich phase. The pH of the media, and consequently the charged/non-charged state of the alkaloids, as well as the hydrophobicity of the molecules, do not alter the extraction pattern observed. These results indicate that the IL ability to form micelles in ATPS is the interfacial phenomenon that creates the trendshift observed in the partition coefficients.