Soft stone masonry, such as tuff stone masonry, is widely used in historical buildings located in, for instance, the Euro-Mediterranean region, in the form of both vaults and load-bearing walls. The development and validation of advanced numerical models, able to realistically simulate the expected damage patterns, failure modes and load-bearing capacity to multiple loading conditions, may significantly contribute to assessment and conservation efforts. Within this study, a simplified micro-modelling approach is implemented in an Applied Element Method (AEM) framework to replicate experimental data at prism, wallet and wall system scales. Thus, bond patterns are simulated by means of rigid units, and all nonlinearities are lumped into zero-thickness contact interfaces. Nonlinear analyses under large displacements are carried out, capturing the experimental behaviour in terms of damage distribution and load-displacement relationships. Complex failure modes involving joint sliding, unit crushing and element rocking are also simulated. The validated numerical models may be used for structural analysis and assessment of larger-scale structures, such as historical buildings.