Historical masonry structures during the decades, were composed with a variety of brick and mortar types according to materials availability of each region and the desirable mechanical properties in each specific case. Different composition of mortars leads to another masonry behavior, and each one is suited for different structural purposes. A crucial aspect in damage evaluation of masonry structures is the analysis of long-term behavior which has a great influence on safety assessment of these structures. In this study, cement, hybrid lime cement, hydraulic lime and lime hydrate mortars were assembled with solid red clay bricks to compose four masonry walls of dimensions 515x376x90 mm. They were tested under cyclic compression loading. Acoustic Emission (AE) allowed in situ monitoring of damage progression. AE is a powerful non-destructive technique applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate a variety of characteristics during fracture propagation to obtain information on the criticality of the ongoing process. Specifically, analyzing and comparing AE parameters among the loading cycles of each wall specimen and among the different masonry compositions, an integrity assessment can be achieved. Furthermore, in each loading and unloading step, pulse velocity measurements were conducted using the AE apparatus in order to gain a velocity distribution mapping among the sensors. Each sensor was pulsed in turn, with all other sensors acting as receivers, generating a velocity matrix from one sensor to another. This provided an insight into the damage severity of masonry walls with the increasing number of loading cycles. This measurement was also necessary for refining AE source location accuracy by using either the horizontal or the vertical velocity. Two different cases were investigated. The use of one uniform velocity for the whole masonry wall and the assumption that the velocity differs in the two vertical directions due to the heterogeneity of the structure. These two cases result in differences in the quantity and the position of the localized events. Furthermore, applying direct ultrasonic pulse velocity measurements, in the direction of the width of masonry walls, another integrity investigation was feasible. The presented results further demonstrate the relationships between AE parameter-based analysis, velocity distribution and source location during cyclic compressive loading in masonry specimens. The identification of the nature of damage through the entire dataset of all sensor arrays provides a promising example for structural health monitoring applications on larger scale masonry specimens. As a conclusion, AE activity analysis proved to be a very efficient approach to evaluate fracture progress in masonry.