In this paper, we present the concept of double-phase microaggregation as an improvement of classical microaggregation for the protection of privacy in distributed scenarios without fully trusted parties. We apply this new concept in the context of mobile health and we show that a distributed architecture consisting of patients and several intermediate entities can apply it to protect the privacy of patients, whose data are released to third parties for secondary use. After recalling some fundamental concepts of statistical disclosure control and microaggregation, we detail the distributed architecture that allows the private gathering, storage, and sharing of biomedical data. We show that double-phase multivariate microaggregation properly fits the needs for privacy preservation of biomedical data in the distributed context of mobile health. Moreover, we show that double-phase microaggregation performs similarly to classical microaggregation in terms of information loss, disclosure risk, and correlation preservation, while avoiding the limitations of a centralized approach.