The phrase "difference in the way" means that there is a distinct variation or contrast in how two or more things are done or perceived. Full definition
He wrote that what appears to be random behavior is actually the result of differences in the way people prefer to use their mental capacities. (verilymag.com)
Books influence people and I think they make a huge difference in the way children see the world and the adults they grow up to be. (author-network.com)
There is a big difference in the way soy is processed. (utne.com)