Isothermal calorimetry (ITC) was used to investigate solvent-free enzymatic biodiesel production. The transesterification of rapeseed oil with methanol and ethanol was catalyzed by immobilized lipase Novozym 435 at 40 °C. The aim of the study was to determine reaction enthalpy for the enzymatic transesterification and to elucidate the mass transfer and energetic processes taking place. Based on the measured enthalpy and composition change in the system, the heat of reaction at 40 °C for the two systems was determined as −9.8 ± 0.9 kJ/mole biodiesel formed from rapeseed oil and methanol, and −9.3 ± 0.7 kJ/mole when rapeseed oil and ethanol was used. Simple Michaelis–Menten kinetics was not an appropriate choice for describing the kinetics of this heterogeneous system. The experiments demonstrated the possibility of investigating complex reaction mixtures using ITC. Although it is possible to determine thermodynamic properties such as reaction enthalpy and reaction rate, the difficulty in actually measuring the true non-mass-transfer-limited reaction kinetics is exposed by the high time resolution of ITC.