A growing number of collaborative applications are being built on top of Peer-to-Peer (P2P) networks which provide scalability and support dynamic behavior. However, the distributed algorithms used by these applications typically introduce multiple communications and interactions between nodes. This is because P2P networks are constructed independently of the underlying topology, which may cause high latencies and communication overheads. In this paper, we propose a topology-aware approach that exploits physical topology information to perform P2P distributed data reconciliation, a major function for collaborative applications. Our solution (P2P-Reconciler-TA) relies on dynamically selecting nodes to execute specific steps of the algorithm, while carefully placing relevant data. We show that P2P-Reconciler-TA introduces a gain of 50% compared to P2P-Reconciler and still scales up.