A soil carbon assessment was performed comparing agricultural cropping systems with natural vegetation along a sampling transect spanning different agro-ecologies on the eastern foot slopes of Mount Kenya in Embu county, 125 km from Nairobi, Kenya. The aim was to determine differences in soil carbon stocks and carbon recalcitrance and relate these to soil textural class, altitude, climatic parameters and land use. Soils from main agricultural systems as tea, coffee and maize-based intercropping, as well as from natural vegetation cover were sampled in triplicates, in five layers from 0 to 30 cm in depth and processed for total carbon analysis. The whole soil samples were also analysed using Laser-Induced Fluorescence Spectroscopy (LIFS) to assess carbon humification. Prototype portable equipment intended for future in situ analysis was used in the lab to ascertain the structure of the most recalcitrant and stable carbon present in different agro-ecosystems. In addition, Near Infrared Spectroscopy (NIRS) was tested for the quantitative analysis of soil carbon, showing that it is a reproducible and low-cost method that provided satisfactory results under the processing conditions of the samples. Results showed wide variation in the level and quality of carbon stored in the soils, depending on soil texture, land use, elevation, climate, agricultural practices and land use history. Considering the heterogeneous nature of sampled soils and the performance of NIRS and LIFS, these results can be used as a basis for the development of fully portable systems able to provide rapid, clean and potentially cost-effective relevant information for soil management.