The investigations focused on the façade of the 17th-century Myszkowskis chapel at the 13th-century Church of the Holy Trinity in Cracow, Poland. Most of the chapel’s façade is made of rusticated limestone blocks, but its lower part is covered with cement render, and the basement consists of irregular pieces of limestone and sandstone, bound and partly replaced with cement mortar. The façade exhibited clearly visible damages: gray soiling of the surface, cracks, scaling, and efflorescence. The study presents characteristics of the cement render and mortar used for stone repair and/or substitution, as well as efflorescence from the lower part of the Myszkowskis chapel façade. The materials were analyzed with optical microscopy, scanning electron microscopy (SEM-EDS), Raman microspectroscopy, X-ray diffractometry (XRPD), and mercury intrusion porosimetry. The analyses demonstrated that the render covering some of the decayed limestone blocks was prepared using Portland cement (residual clinker grains represent alite and belite) as a binding agent, mixed with crushed stone as an aggregate. The cement mortar consisted of rounded quartz grains, rock fragments, and feldspars in very fine-grained masses of calcite and gypsum, also containing relics of cement clinker (alite, belite, ferrite, and aluminate). All these components point out the use of the ordinary Portland cement. Analyses of the efflorescence allowed us to distinguish several secondary salts, among others, thenardite, aphthitalite, and darapskite. The appearance of these phases is related to the composition and physicochemical properties of the building materials, atmospheric alteration agents, air pollution, and some other anthropogenic factors.