The efficient and environmentally sustainable separation process for rare earth elements (REE), especially for adjacent lanthanoids, remains a challenge due to the chemical similarity of REEs. Tetravalent actinoids, thorium, and traces of uranium are also present in concentrates of REEs, making their separation relevant. This study reports six simple water-soluble aminobis(phosphonate) ligands, RN[CH2P(O)(OH)2]2 (1 R = CH2CH3, 2 R = (CH2)2CH3, 3 R = (CH2)3CH3, 4 R = (CH2)4CH3, 5 R = (CH2)5CH3, 6 R = CH2CH(C2H5)(CH2)3CH3) as precipitating agents for REEs, Th, and U, as well as gives insight into the coordination modes of the utilized ligands with REEs at the molecular level. Aminobis(phosphonates) 4–6 with longer carbon chains were found to separate selectively thorium, uranium, and scandium from REEs with short precipitation time (15 min) and excellent separation factors that generally range from 100 to 2000 in acidic aqueous solution. Ligands 1–6 also improved separation factors for adjacent lanthanoids in comparison to traditional oxalate precipitation agents. Importantly, precipitated metals can be recovered from the ligands with 3 molar HNO3 with no observed ligand decomposition enabling the possibility of recycling the ligands in the separation process. NMR-monitored pH titrations for 1 showed deprotonation steps at pKa 1.3, 5.55, and >10.5, which indicate that the ligands remain in a deprotonated [L]−1 form in the pH range of 0–4 used in the precipitation studies. 31P NMR titration studies between 1 and M(NO3)3 (M = Y, La, Lu) gave satisfactory fits for 1:3, 1:2, and 1:1 metal–ligand stoichiometries for Y, La, and Lu, respectively, according to an F-test. Therefore, aminobis(phosphonate) precipitation agents 1–6 are likely to form metal complexes with fewer ligands than traditional separation agents like DEHPA, which coordinates to REEs in 1:6 metal–ligand ratio.