New insoluble layered zirconium phosphate carboxyaminophosphonates (ZPs), with the general formula Zr2(PO4)H5[(O3PCH2)2N(CH2)nCOO]2·mH2O (n = 3, 4, and 5), have been prepared and characterized. The crystal structure for n = 3 and 4 samples was determined ab initio from X-ray powder diffraction data. The structure for n = 3 was monoclinic in space group C2/c with the following unit cell parameters: a = 34.346(1) Å, b = 8.4930(2) Å, c = 9.0401(2) Å, and β = 97.15(1)°. The structure for n = 4 was triclinic in space group P1̅ with the following unit cell parameters: a = 17.9803(9) Å, b = 8.6066(4) Å, c = 9.0478(3) Å, α = 90.466(3)°, β = 94.910(4)°, and γ = 99.552(4)°. The two structures had the same connectivity as Zr phosphate glycine diphosphonate (n = 1), as previously reported. By intercalation of short amines, these layered compounds were exfoliated in single lamella or packets of a few lamellae, which formed colloidal dispersions in water. After a thorough characterization, the dispersed lamellae were functionalized with Ag nanoparticles, which were grown in situ on the surface of exfoliated lamellae. Finally, their antimicrobial activity was tested on several Gram-positive and Gram-negative bacteria. All of these systems were found to be active against the four pathogens most frequently isolated from orthopedic prosthetic infections and often causative of nosocomial infections. Interestingly, they were found to express powerful inhibitory activity even against bacterial strains exhibiting a relevant profile of antibiotic resistance such as Staphylococcus aureus ATCC 700699.