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We report on the structural and vibrational properties of Co nanoparticles formed by ion implantation and thermal annealing in amorphous silica. The evolution of the nanoparticle size, phase, and structural parameters were determined as a function of the formation conditions using transmission electron microscopy, small-angle x-ray scattering, and x-ray absorption spectroscopy. The implantation fluence and annealing temperature governed the spherical nanoparticle size and phase. To determine the latter, x-ray absorption near-edge structure analysis was used to quantify the hexagonal close packed, face-centered cubic and oxide fractions. The structural properties were characterized by extended x-ray absorption fine structure spectroscopy (EXAFS) and finite-size effects were readily apparent. With a decrease in nanoparticle size, an increase in structural disorder and a decrease in both coordination number and bondlength were observed as consistent with the non-negligible surface-area-to-volume ratio characteristic of nanoparticles. The surface tension of Co nanoparticles calculated using a liquid drop model was more than twice that of bulk material. The size-dependent vibrational properties were probed with temperature-dependent EXAFS measurements. Using a correlated anharmonic Einstein model and thermodynamic perturbation theory, Einstein temperatures for both nanoparticles and bulk material were determined. Compared to bulk Co, the mean vibrational frequency of the smallest nanoparticles was reduced as attributed to a greater influence of loosely bonded, undercoordinated surface atoms relative to the effect of capillary pressure generated by surface curvature.