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Why does my pudding or yoghurt loses its structure when I use fresh pineapple ?

Pineapples and a few other fruits (such as kiwi and papaya) contain active protein-degrading enzymes or proteases. Pineapples contain bromelain, in papaya the enzyme is called papain. These enzymes are still active at low (refrigeration) temperatures and degrade the proteins in pudding or yoghurt. The consistency of yogurt is largely determined by milk proteins, pudding is often made with gelatine, a gelating protein. When you add fresh pineapple to these products the proteins are degraded and the structure is lost. The taste is also affected; the degradation products have a bitter taste.

The enzymes are heat sensitive. By heating the fruits (blanching in boiling water or in the microwave), the activity is lost and the fruits can be used in the yoghurt or pudding.