Let $Y$ be a (partial) minimal model of a scheme $V$ with a cluster structure. Under natural assumptions, for every choice of seed we associate a Newton--Okounkov body to every divisor on $Y$ supported on $Y \setminus V$ and show that these Newton--Okounkov bodies are positive sets in the sense of Gross, Hacking, Keel and Kontsevich \cite{GHKK}. This construction essentially reverses the procedure in loc. cit. that generalizes the polytope construction of a toric variety to the framework of cluster varieties. In a closely related setting, we consider cases where $Y$ is a projective variety whose universal torsor $\text{UT}_Y$ is a partial minimal model of a scheme with a cluster structure of type $\mathcal A$. If the theta functions parametrized by the integral points of the associated superpotential cone form a basis of the ring of algebraic functions on $\text{UT}_Y$ and the action of the torus $T_{\text{Pic}(Y)^*}$ on $\text{UT}_Y$ is compatible with the cluster structure, then for every choice of seed we associate a Newton--Okounkov body to every line bundle on $Y$. We prove that any such Newton--Okounkov body is a positive set and that $Y$ is a minimal model of a quotient of a cluster $\mathcal A$-variety by the action of a torus. Our constructions lead to the notion of the intrinsic Newton--Okounkov body associated to a boundary divisor in a partial minimal model of a scheme with a cluster structure. This provides a wide class of examples of Newton-Okoukov bodies exhibiting a wall-crossing phenomenon in the sense of Escobar--Harada \cite{EH20}. This approach includes the partial flag varieties that arise as minimal models of cluster varieties. For the case of Grassmannians, our approach recovers, up to interesting unimodular equivalences, the Newton--Okounkov bodies constructed by Rietsch--Williams in \cite{RW}.