Isothermal microcalorimetry is a sensitive non-invasive analytical tool that can become useful in research on compost and other biosolids. The aim of the present study was to address several methodological aspects that are critical to the use of microcalorimetry to assess the dynamics of microbial activity in such systems. The results show that: (1) The calorimetric baseline is strongly influenced by the run temperature in the range relevant to composting systems (20-60 degrees C), and is also affected by addition of the water that is required to maintain or optimize microbial activity, presumably because some water evaporates through ampoule gaskets. (2) Amending mature compost with readily available substrates requires additional careful baseline treatment. (3) Sample heterogeneity can be successfully minimized by passing through a 2-mm sieve. Additional size separation can be useful to enable focusing on the more active fractions. (4) Oxygen depletion is a key feature in batch calorimetric analysis; for samples of highly active composts or manure, the total amount of heat released relative to the oxygen available in the ampoule may indicate the co-existence of anaerobic and aerobic metabolic pathways. Finally, practical recommendations for microcalorimetry analyses of pre-mature and mature composts are outlined.