Although the exact cause of delayed onset muscle soreness is not thoroughly understood; evidence suggests a proposed model of why it occurs:
First, strenuous muscle contractions are thought to cause structural damage to the muscle. Whereas eccentric contractions are thought to cause more damage than concentric contractions.
Secondly membrane damage may occur which includes damage to the sarcoplasmic reticulum. In turn, this could cause calcium to leak and collect in the mitochondria which would inhibit the production of ATP.
The buildup of calcium may also activate specific enzymes which degrade cellular proteins. The combination of membrane damage and muscle protein breakdown results in an inflammatory response that increases the production of prostaglandins, histamines, and free radicals.
Finally, the build-up of these histamines and the swelling around the muscle fibers stimulate pain receptors which could result in feeling pain in the muscle.