The Maritime Continent (MC) forms the western boundary of the tropical Pacific Ocean, and relatively small changes in this region can impact the climate locally and remotely. In the mid-Piacenzian warm period of the Pliocene (mPWP; 3.264 to 3.025 Ma) atmospheric CO2 concentrations were ∼ 400 ppm, and the subaerial Sunda and Sahul shelves made the land–sea distribution of the MC different to today. Topographic changes and elevated levels of CO2, combined with other forcings, are therefore expected to have driven a substantial climate signal in the MC region at this time. By using the results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), we study the mean climatic features of the MC in the mPWP and changes in Indonesian Throughflow (ITF) with respect to the preindustrial. Results show a warmer and wetter mPWP climate of the MC and lower sea surface salinity in the surrounding ocean compared with the preindustrial. Furthermore, we quantify the volume transfer through the ITF; although the ITF may be expected to be hindered by the subaerial shelves, 10 out of 15 models show an increased volume transport compared with the preindustrial. In order to avoid undue influence from closely related models that are present in the PlioMIP2 ensemble, we introduce a new metric, the multi-cluster mean (MCM), which is based on cluster analysis of the individual models. We study the effect that the choice of MCM versus the more traditional analysis of multi-model mean (MMM) and individual models has on the discrepancy between model results and data. We find that models, which reproduce modern MC climate well, are not always good at simulating the mPWP climate anomaly of the MC. By comparing with individual models, the MMM and MCM reproduce the preindustrial sea surface temperature (SST) of the reanalysis better than most individual models and produce less discrepancy with reconstructed sea surface temperature anomalies (SSTA) than most individual models in the MC. In addition, the clusters reveal spatial signals that are not captured by the MMM, so that the MCM provides us with a new way to explore the results from model ensembles that include similar models.