This paper explores the seismic fragility assessment of historical masonry buildings in the context of performance-based earthquake engineering, using multiple-record incremental dynamic analyses (MR-IDA). The methodology is applied to two case studies, the first being a stiff monumental structure, and the second a tall and slender 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. Simultaneously, 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 records 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. The fragility functions accounting for the uncertainties arising from the record-to-record variability are contrasted against 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 presented 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 obtained from the cloud-based approach using unscaled records.