Yes, there is a difference.
The issue of food intolerances is very complex. That is why there are often ambiguities of definition in colloquial language, but also in the literature.
Food intolerances are an excessive reaction of the immune system to specific protein components of certain foods.
For example gluten is a protein component of certain cereals, casein is the main protein component of animal milk products.
Intolerances, in contrast to intolerances, are due to an insufficient (enzymatic) digestive process or insufficient absorption of nutrients in the intestine (malabsorption) or a pseudoallergy.
The best known forms of intolerance are lactose and fructose intolerance and histamine intolerance