The present work focuses on the use of protic ionic liquids (PILs) in the formation of blphasic phase systems with acetonitrile, followed by a study of the partitioning of alkaloids such as caffeine, theobromine and theophylline between the phases. Initially, new phase diagrams were built at 298.15 K and atmospheric pressure to observe the ease of phase formation. All PILs were able to form biphasic systems with acetonitrile, except for those based on pentanoate as anion. From these studies, the order of ease of formation was estimated using the logarithm of the distribution coefficient of system constituents; acetate was the most apt to form biphasic systems. Furthermore, the replacement of amine hydrogen (ethanolamine) by methyl or 2-hydroxymethyl group did not alter the ease of phase formation. All alkaloids (caffeine - CF, theobromine - TB and theophylline - TF) migrated to the bottom phase (PIL-rich phase) due to their higher hydrophilicity, where good recovery rates were verified (CF: 61%, TB: 71% and TF: 69%).