In this paper, we study the structure of braid graphs in simply-laced Coxeter systems. We prove that every reduced expression has a unique factorization as a product of so-called links, which in turn induces a decomposition of the braid graph into a box product of the braid graphs for each link factor. When the Coxeter graph has no three-cycles, we use the decomposition to prove that braid graphs are partial cubes, i.e., can be isometrically embedded into a hypercube. For a special class of links, called Fibonacci links, we prove that the corresponding braid graphs are Fibonacci cubes.