Dumas, Foucaud, Perez and Todinca (2024) recently proved that every graph whose edges can be covered by $k$ shortest paths has pathwidth at most $O(3^k)$. In this paper, we improve this upper bound on the pathwidth to a polynomial one; namely, we show that every graph whose edge set can be covered by $k$ shortest paths has pathwidth $O(k^4)$, answering a question from the same paper. Moreover, we prove that when $k\leq 3$, every such graph has pathwidth at most $k$ (and this bound is tight). Finally, we show that even though there exist graphs with arbitrarily large treewidth whose vertex set can be covered by $2$ isometric trees, every graph whose set of edges can be covered by $2$ isometric trees has treewidth at most $2$.