Phosphonic and carboxylic fluorescent nanoparticles have been fabricated by direct reprecipitation in water. Their fluorescence properties strongly differ from those of the corresponding esters where strong H-bonding formation is prohibited. Comparative experiments between the two acid derivatives, differing only in their acid functions while keeping the same alkyl chain, have evidenced the peculiar behavior of the phosphonic acid derivative compared to its carboxylic analog. A dramatic emission quenching for the phosphonic acid in aprotic toluene could be observed while a fivefold increase in the fluorescence signal was observed for molecules assembled as nanoparticles. Such properties have been attributed on the theoretical basis to the formation of folded conformers in solution, leading to deactivation of the radiative excited state through intramolecular H-bonding. These studies evidence for the first time through time-resolved fluorescence measurements the stronger H-donating character of phosphonic acids compared to the carboxylic ones, and provide information on the degree of structural heterogeneity within the nanoparticles. They should pave the way for the rational fabrication of chelating acid fluorophores, able to complex metal oxides to yield stiff hybrid magnetofluorescent nanoparticles which are attracting considerable attention in the growing fields of bimodal imaging and vectorization applications.