The problems inherent to shelter design for archaeological sites are explored in the case study of the preliminary schematic design proposals for a permanent shelter for Building 5 at the Minoan site of Palaikastro, Crete. Although the facades of Building 5 are constructed of rubble stone and ashlar, it also contains earthen construction in the form of interior partitions and an earthen stair. A temporary shelter was erected immediately after excavation in 1990 while the physical and chemical characterization of the earthen materials was performed. Based on conclusions resulting from the materials analyses, archaeological evidence and research in Minoan architectural typologies, solutions for a permanent shelter were conceptualized. The methodology and criteria for the evaluation and design of the permanent shelter are discussed along with the evolution of the actual design proposals.