A mobile soil mapping system includes an implement for traversing a field to be mapped, and a reflectance module carried by the implement for collecting spectroscopic measurements of soil in the field. The reflectance module has a light source, an optical receiver for transmitting light to a spectrometer, and a shutter system that alters the optical path between the light source and the optical receiver. The shutter system allows the system to automatically collect a dark reference measurement and a known reference material measurement at timed intervals to compensate for drift of the spectrometer and the light source. A self-cleaning window on the reflectance module has a lower surface maintained in firm contact with the soil during operation. External reference blocks are used to calibrate the system to ensure standardized, repeatable data. Additional sensors are carried by the implement to collect other soil data, such as electrical conductivity and temperature.