The cement sector is currently one of the main sources of carbon dioxide released into the atmosphere, contributing around 5–8% of the total CO2 emissions. The partial replacement of cement with supplementary cementitious materials (SCMs) in mortar provides an opportunity to produce environment-friendly and economical mortars. In this study, two types of clay were collected from two different locations in Oman, namely Quriyat (QRT-3) and Nizwa (NZW-5). These clays have undergone several processes, including grinding and sieving to produce particles smaller than 75 μm, and are then subjected to physical, chemical, and thermal tests to classify the clay. The chemical analysis demonstrated that the sum of (SiO2+ Al2O3+ Fe2O3) in QRT-3 equals 55.7%, and the percentage of CaO equals 26.75%, qualifying it as cementitious and pozzolanic material. While the sum of (SiO2+ Al2O3+ Fe2O3) in NZW-5 equals 84.4%, and the percentage of CaO equals 6.4%, qualifying it as pozzolanic material. Thermogravimetric and differential thermal analysis showed that the suitable calcination temperatures of QRT-3 are 740 °C and 820 °C, while for NZW-5 clay are 720 °C and 760 °C. The calcined clay was used to replace part of the Portland cement in the mortar with a fixed water-to-cement ratio (w/c) of 0.40. The efficiency of the addition of calcined clay (QRT-3 and NZW-5) in mortar was evaluated in two different stages. The first stage includes replacing cement with different percentages of 10%, 20%, 25%, and 30% of QRT-3 clay or NZW-5 clay. The second stage includes using the optimum replacement level and calcination temperature based on the 28-day highest compressive strength of the binary mortar mixes. As a result, 740 °C and 760 °C calcination temperatures with 10% of calcined clay as a replacement for cement were selected for the composite mortar mixes. Binary and composite mortar mixes were tested to check the fresh and hardened properties. Different tests were conducted on fresh mortar, such as temperature, flowability, and fresh density. In addition, several tests were conducted on hardened mortar, such as compressive strength, flexural strength, porosity and absorption, ultrasonic pulse velocity (UPV), fire resistance, and acid and sulfate resistance. The results show that replacing cement with different percentages of QRT-3 or NZW5 clays increased the normal consistency and setting times. The addition of calcined clay (QRT-3 or NZW-5) reduced the flow diameter and required the same or a greater amount of superplasticizer dosage to achieve the desired levels of flowability. The optimal percentage was found at 10% of QRT-3 calcined at 740 °C and 10% of NZW5 calcined at 760 °C, which provided higher compressive strength at 7, 28, and 91 days than the control mortar. However, there is no improvement in flexural strength for most binary and all composite mixes. The UPV results demonstrated a minor improvement in the UPV values by 0.75% to 5.5% for all binary mixes containing clay calcined at 820 °C, 720 °C, and 760 °C. Most modified mortar mixes exhibited a decrease in porosity and water absorption. In addition, good outcomes in the residual strength can be observed in some binary mixes compared to the control mortar after 2 hours of exposure to 800 °C in an electrical furnace. Generally, blended mortars showed different behaviours in terms of increase or decrease in weight and strength compared to the control mortar when exposed to acids for 9 weeks. The 20% QRT-3 mortar mix calcined at 740 °C provides good resistance to acid when exposed to hydrochloric, nitric, sulfuric, and acetic acids compared to the control mortar. All blended mortar mixes showed lower compressive strength than the control mortar after exposure to the phosphoric acid solution. Most binary mixes demonstrated better resistance to 5% of sodium sulphate + 5% of sodium chloride than the control mortar.