Abstract Fourier Transform Infrared (FTIR) spectroscopy is a commonly-used technique for investigating diamonds, that gives the most useful information if spatially-resolved measurements are used. In this paper we discuss the best way to acquire and present FTIR data from diamonds, using examples from Murowa (Zimbabwe), Argyle (Australia) and Machado River (Brazil). Examples of FTIR core-to-rim line scans, maps with high spatial resolution and maps with high spectral resolution that are fitted to extract the spatial variation of different nitrogen and hydrogen defects are presented. Model mantle residence temperatures are calculated from the concentration of A and B nitrogen-containing defects in the diamonds using known times of annealing in the mantle. A new, two-stage thermal annealing model is presented that better constrains the thermal history of the diamond and that of the mantle lithosphere in which the diamond resided. The effect of heterogeneity within the analysed FTIR volume is quantitatively assessed and errors in model temperatures that can be introduced by studying whole diamonds instead of thin plates are discussed. The spatial distribution of VN3H hydrogen defects associated with the 3107 cm− 1 vibration does not follow the same pattern as nitrogen defects, and an enrichment of VN3H hydrogen at the boundary between pre-existing diamond and diamond overgrowths is observed. There are several possible explanations for this observation including a change in chemical composition of diamond forming fluid during growth or kinetically controlled uptake of hydrogen.