Forty-two mortar samples, from two archaeological excavations located in Sagunto (Valencian Community, Spain), were analysed by both portable energy dispersive X-ray fluorescence spectroscopy (pED-XRF) and inductively coupled plasma mass spectrometry (ICP-MS) to determine major and minor elements and traces including rare earth elements (REEs). Collected data were crossed with those previously obtained from Sagunto Castle mortars, and principal component analysis (PCA) was applied to discriminate the construction phases of the unearthed buildings. REE permitted to ascribe most of the masonries to the Roman Imperial period. Moreover, a statistical model was built by employing partial least squares discriminant analysis (PLS-DA) in order to classify the mortars from Roman Imperial period and from Islamic period due to the problematic overlapping between these two phases. Results confirmed the effectiveness of the developed indirect chronology method, based on REE data, to discriminate among historic mortars from different construction periods on a wide scale including different Sagunto archaeological sites.