This paper demonstrates the application of in situ diagnostic tools to document stone heritage sites prior to conservation interventions using a Medieval ruin of Central Europe (Székesfehérvár, Hungary). The applied methods included lithological mapping and characterisation and mapping of decay forms as well as in situ measurements of physical parameters such as Schmidt hammer rebound, moisture content and micro-drilling resistance. The combination of these methods allowed the condition assessment of different lithotypes and demonstrated the role of micro-fabric, mineralogical composition and climatic conditions in stone durability. Differences were found in the properties and in the weathering forms of fine-grained and medium-grained porous oolitic limestone and travertine. The black crust observed in porous limestone is less prone to detachment on medium-grained oolitic limestone ashlars, while scaling was observed on fine-grained oolitic limestone blocks. The micro-drilling resistance of exposed porous limestone showed higher drilling resistance at the crust zone (upper 1–2 mm) than below, marking the upper cemented zone, while the drilling resistance of porous limestone under shelter showed an opposite trend. The shelly limestone, the sandy calcarenite and red compact limestone also showed an increase in drilling resistance at the topmost app. 2 mm zone. The applied in situ, non-invasive and micro-destructive techniques helped in the identification of endangered zones at Székesfehérvár, thus, they can provide key information on condition assessment of stones at heritage sites, where sampling is limited and preventive conservation is important.