Being a country exposed to strong seismicity, the estimation of seismic hazard in Tajikistan is essential for urbanized areas, such as the rapidly growing capital city Dushanbe. To ensure people’s safety and adequate construction work, a detailed seismic microzonation is the key to proper hazard planning. Existing estimations of seismic hazard date back to 1978; they are based on engineering geological investigations and observed macroseismic data. Thereupon relies the Tajik Building Code, which considers seismic intensities according to the Medvedev–Sponheuer–Karnik Scale, MSK-64. However, this code does not accurately account for soil types, which vary considerably in Dushanbe—not only by their nature, but also due to increasing anthropogenic influences. In this study, we performed a series of analyses based on microtremor array measurements, seismic refraction tomography, and instrumental data recording from permanent stations for standard spectral ration and from mobile seismic stations for the horizontal to vertical spectral ratio in order to provide a comprehensive full-cover microzonation of Dushanbe accounting for soil types. Our results identify several critical areas where major damage is likely to occur during strong earthquakes.