Replicating data fragments in Linked Data improves data availability and performances of federated query engines. Existing replication aware federated query engines mainly focus on source selection and query decomposition in order to prune redundant sources and reduce intermediate results thanks to data locality. In this paper, we extend replication-aware federated query engines with a replication-aware parallel join operator: PeNeLoop. PeNeLoop exploits redundant sources to parallelize the join operator and reduce execution time. We implemented PeNeLoop in the federated query engine FedX with the replicated-aware source selection Fedra and we empirically evaluated the performance of FedX+Fedra+PeNeLoop. Experimental results suggest that FedX+Fedra+PeNeLoop outperforms FedX+Fedra in terms of execution time while preserving answer completeness.