Phosphonates and carboxylates are two primitive functional groups omnipresent in nature, and they act as good chelators for metal ion binding. These two functional groups are always associated with dissociable protons in their acidic forms. Thus, their interactions are associated with protonation/deprotonation mechanisms. The present study was aimed at determining the thermodynamic parameters (log KP/pKa, ΔGP, ΔHP, and ΔSP) for the protonation of three aliphatic phosphonocarboxylates, namely, phosphonoformic acid (PFA), phosphonoacetic acid (PAA), and phosphonopropanoic acid (PPA), which differ in their spacer (connecting −CH2 moiety) length. Potentiometric and isothermal titration calorimetric studies were employed to determine the protonation constants (log KP/pKa) and enthalpies (ΔHP) of the three phosphonocarboxylates. All of the acids have three protonation sites ranging in pKa values from 1.8 to 7.4. The enthalpies of protonation are close to ±5 kJ/mol, except for the third protonation, and these protonations are mainly entropy-driven interactions. Density functional theory calculations were carried out to estimate interatomic distances and partial charges on all of the atoms to gain insights into the protonation mechanism at the molecular level. The predicted theoretical estimations followed the experimentally observed protonation trends.