This work characterizes ancient mortars used in construction of the Bronze Age Minoan port at Kommos in Crete. The port dates from c. 1850 BCE with port facilities at the harbor and residences on the Central hillside and the Hilltop. A Greek, Phoenician, and Roman sanctuary overlies the administrative center. The first step collected representative samples from the different construction phases, previous conservation interventions, exposure to different environmental factors, and different material composition. From these 10 mortar samples were analyzed using stereo- and digital microscopy, X-ray diffraction (XRD), X-ray Fluorescence (XRF), and Fourier Transform Infrared spectroscopy (FTIR) to determine texture, morphology, mineralogical, and physico-chemical properties. The physico-chemical and mineralogical analyses divided the samples into two groups: lime binder mortars and earthen binder mortars. The main minerals identified in the samples are calcite, quartz, dolomite, illite, albite, kaolinite, and vermiculite. Analysis of local clay showed that local materials were used in the production of these mortars. The analysis of mortar samples with stereomicroscopy, XRF, and FTIR showed that the samples are mainly composed of calcite and silicates in major quantities along with aluminum, magnesium, and iron oxide in minor quantities. A wide variety of local aggregates and ceramic fragments were used in the production of these ancient mortars. The mortar condition resulted in a decay state that needs conservation interventions. This characterization of the ancient mortars was important for the design of compatible restoration mortars.