Here, we investigate the effects of exercise training on glucose‐ and cholinergic‐induced insulin secretion in pancreatic islets from obese and lean rats. Male Wistar rats were treated with monosodium glutamate (MSG) for the first 5 days of life, while control (CON) rats received saline. At 21 days, the rats were divided into exercised (EXE) and sedentary (SED) groups. The EXE rats swam for 30 minutes, three times/week, for 10 weeks. After this, MSG‐SED rats showed hyperglycaemia, hypertriglyceridaemia and hyperinsulinaemia. Besides, islets from MSG‐SED rats exhibited increased glucose‐stimulated insulin secretion (GSIS), followed by impaired glucose sensitivity, absence of glucose‐amplifying pathway and weak cholinergic response. In contrast, adiposity, hyperinsulinaemia and hypertriglyceridaemia were reduced in MSG‐EXE rats. Moreover, islets from MSG‐EXE rats exhibited lower GSIS and improved islet glucose sensitivity, without restoration of the glucose‐amplifying pathway or alteration in the weak cholinergic effect of these islets. In islets from CON‐EXE rats we also observed reduced GSIS and absence of glucose‐amplifying effects and an accentuated reduction in cholinergic insulinotropic responses, without effect on glucose sensitivity in pancreatic islets from this group. Neither obesity nor exercise modified Muscarinic Receptor 3 (M3R) immunocontent or its downstream pathways (PKC and PKA). Moreover, only CON‐EXE showed increased GSIS in the presence of calcium blocker, Thapsigargin. In conclusion, swimming training reduces GSIS and cholinergic responsiveness in isolated pancreatic islets from lean and hypothalamic obese rats, which could be due to the inhibition of glucose‐amplifying pathways.