Multichannel magnetocardiography (MCG) during exercise testing has been shown to detect myocardial ischaemia in patients with coronary artery disease. Previous studies on exercise MCG have focused on one or few time intervals during the recovery period and only a fragment of the data available has been utilized. We present a method for beat-to-beat analysis and parametrization of the MCG signal. The method can be used for studying and quantifying the changes induced in the MCG by interventions. We test the method with data recorded in bicycle exercise testing in healthy volunteers and patients with coronary artery disease. Information in all cardiac cycles recorded during the recovery period of exercise MCG testing is, for the first time, utilized in the signal analysis. Exercise-induced myocardial ischaemia was detected by heart rate adjustment of change in magnetic field map orientation. In addition to the ST segment, the T wave in the MCG was also found to provide information related to myocardial ischaemia. The method of analysis efficiently utilizes the spatial and temporal properties of multichannel MCG mapping, providing a new tool for detecting and quantifying fast phenomena during interventional MCG studies. The method can also be applied to an on-line analysis of MCG data.