Silver nanoparticles are usually prepared by the reduction of silver cations through chemical and non-sustainable procedures that involve the use of reducing chemical agents. Therefore, many efforts have been made in the search for sustainable alternative methods. Among them, an ultrasound-assisted procedure could be a suitable and sustainable method to afford well-dispersed and nanometric silver particles. This paper describes a sustainable, ultrasound-assisted method using citrate as a reducing agent to prepare silver@hydroxyapatite functionalized calcium carbonate composites. For comparison, an ultrasound-assisted reduction was performed in the presence of NaBH4. The composites obtained in the presence of these two different reducing agents were compared in terms of nanoparticle nature, antimicrobial activity, and cytotoxic activity. The nanoparticle nature was investigated by several techniques, including X-ray powder diffraction, field-emission scanning electron microscopy, transmission electron microscopy, UV–Vis spectroscopic measurements, and X-ray photoemission spectroscopy. Nanoparticles with a predominance of Ag or Ag3PO4 were obtained according to the type of reducing agent used. All composites were tested for antimicrobial and antibiofilm activities against Gram-positive and Gram-negative (Staphylococcus aureus and Pseudomonas aeruginosa, respectively) bacteria and for cytotoxicity towards human skin keratinocytes and human fibroblasts. The nature of the nanoparticles, Ag or Ag3PO4, and their predominance seemed to affect the in vitro silver release and the antimicrobial and antibiofilm activities. The composites obtained by the citrate-assisted reduction gave rise to the best results.