This paper explores the seismic fragility assessment of historical masonry buildings in the context ofperformance-based earthquake engineering, using multiple-record incremental dynamic analyses (MR-IDA). Themethodology is applied to two case studies, the first being a stiff monumental structure, and the second a tall andslender masonry building. Both case studies are modelled in the OpenSees software using three-dimensional macroelements that account for the in-plane (IP) and out-of-plane (OOP) response of masonry walls. Simulta-neously, the numerical models account for the influence of non-linear connections in floor-to-wall interfaces and wall-to-wall interlocking. The record-to-record variability induced by the random nature of the ground motion is addressed through earthquake selection consistent with the variability of European hazard. Ground motion re-cords are normalised at a uniform level of seismic intensity to be sequentially increased for the computation of IDA curves. Once IDA curves and fragility functions are derived, the failure results are thoroughly discussed. Thefragility functions accounting for the uncertainties arising from the record-to-record variability are contrastedagainst the results of the seismic assessments affected by multiple sources of uncertainty in material and modelling parameters from a previous study. Finally, the fragility curves derived from the methodology pre-sented herein are directly compared with fragility functions from probabilistic seismic demand analysis (PSDA). Overall, IDA-based fragility functions are found to provide more conservative predictions than the ones obtainedfrom the cloud-based approach using unscaled records.