Let $p$ and $q$ be distinct prime numbers, with $q\equiv 1\pmod{12}$. Let $N$ be a positive integer that is coprime to $pq$. We prove a formula relating the Hasse--Weil zeta function of the modular curve $X_0(qN)_{\mathbb{F}_q}$ to the Ihara zeta function of the $p$-isogeny graphs of supersingular elliptic curves defined over $\overline{\mathbb{F}_q}$ equipped with a $Γ_0(N)$-level structure. When $N=1$, this recovers a result of Sugiyama.