Heat alters the engineering behavior of soils. Marl soils are highly-erodible sedimentary deposits composed of clay minerals and calcium carbonate. Clay minerals and calcium carbonate in marl soils considerably influence the engineering behavior of such soils. Soils can be exposed to heat for a variety of reasons leading to changes in the physical, mechanical, and microstructural properties, in particular the engineering properties of marl soils. In the design of geo-environmental projects, the results of soil mechanics, especially the permeability coefficient, directly influence the design outcomes. Accordingly, this study aimed at evaluating the effect of heat treatment on the engineering behavior and permeability coefficient of marl soils from a microstructural perspective. To this end, the marl soil was heated to 25–900°C for 2 h. The changes in the engineering properties of marl soils at different temperatures were studied by macrostructural (gradation, Atterberg limits, loss-on-drying, Unconfined Compressive Strength (UCS) and permeability) and microstructural (XRD and SEM) investigations. The results were suggestive of the considerable effect of heat treatment on the engineering behavior of marl soils, as the compressive strength of marl soils increased by 100 folds, and the permeability coefficient reduced by about 6 times at 700°C.