This study is the result of a joint collaboration between the Laboratório Nacional de Engenharia Civil, the University of Evora and the Instituto Português do Património Arquitectónico aiming the establishment of an integrated conservation methodology and the proposal of adequate conservation strategies. Ancient mortars from the Igreja da Misericórdia and Igreja Matriz of Viana do Alentejo (Alentejo, Portugal) have been studied by means of chemical analysis, X-ray diffraction (XRD), simultaneous thermogravimetric and differential thermal analysis (TG-DTA), scanning electron microscopy (SEM) equipped with an energy dispersive X-ray spectrometer (EDS) and optical microscopy. This study showed that the mortars are made of lime and that two types of aggregates were used: sand with a homogeneous composition identical to that from the regional granodiorites and a heterogeneous sand composed of both magmatic and metamorphic rocks, possibly from local fluvial sediments. No pozzolanic materials were identified. The actual chemical and minero-petrographic composition of the mortars was determined.