This work investigates the hydration behaviour and the physico-mechanical properties of mortars based on calcium sulfoaluminate (CSA) cements and fly ash-based geopolymers (GEO) as alternatives to ordinary Portland cement. According to the EN 1504-3, mortars were prepared in order to reach three compressive strength classes, namely R1, R2 and R3 (R1 with Rc = 10 MPa, R2 with Rc = 15 MPa and R3 with Rc = 25 MPa). CSA mortars were prepared by using sulfoaluminate cement alone (R3) or in mixture with a limestone filler (R1 and R2); GEO mortars were manufactured by alkali-activation of coal fly ash and calcium aluminate cement with a sodium silicate and potassium hydroxide water solution. The hydration behaviour was evaluated on pastes submitted to differential thermal-thermogravimetric and X-ray diffraction analyses. Mortars was analysed through mercury intrusion porosimetry; their mechanical properties were evaluated in terms of compressive strength and dynamic modulus of elasticity. Furthermore, capillary water absorption and drying shrinkage tests were carried out in order to evaluate their durability. Due to the rapid ettringite formation, CSA-based mixtures reached their maximum compressive strength values faster than the corresponding GEO mortars. Results showed that the lower modulus of elasticity of GEO mortars causes the higher drying shrinkage. Moreover, the lower porosity exhibited by GEO mortars was responsible for the lower water capillary absorption.