Recently, the application of low salinity water (LSW), nanoparticles (NPs), and surfactants (collectively abbreviated as LNS) in carbonate formations for enhanced oil recovery (EOR) purposes has been under investigation, but relatively few studies have been performed for their implementation in fractured carbonate reservoirs (FCRs). The objective of this study is to apply the recently proposed method of alternatively injecting LNS in cycles into FCRs using silica and zirconia NPs. The cumulative oil recovered from the two coreflooding experiments performed at 3000 psi overburden pressure and 70 °C temperature is reported in this study in addition to spontaneous imbibition (SI) experiments. The experimental design is structured to depict the best industrial practice for the injected fluids in FCRs. Furthermore, this work investigates the effect of zirconia NPs on the interfacial tension (IFT) between the injected fluids and crude oil under the previously stated experimental conditions. The outcome of these experiments divulges that the alternating injection of LNS employing silica and zirconia NPs is effective and well suited for EOR applications in FCRs owing to a cumulative oil recovery of approximately 8 and 7% of the original oil in place (OOIP), respectively. This study validates the implementation of the recently proposed alternating injection of the LNS technique for FCRs and shows its performance utilizing newly acquired zirconia NPs, which is relevant for industrial application at a large scale.