We study toric degenerations arising from Gröbner degenerations or the tropicalization of partial flag varieties. We produce a new family of toric degenerations of partial flag varieties whose combinatorics are governed by matching fields and combinatorial mutations of polytopes. We provide an explicit description of the polytopes associated with the resulting toric varieties in terms of matching field polytopes. These polytopes encode the combinatorial data of monomial degenerations of Plücker forms for the Grassmannians. We give a description of matching field polytopes of flag varieties as Minkowski sums and show that all such polytopes are normal. The polytopes we obtain are examples of Newton-Okounkov bodies for particular full-rank valuations for flag varieties. Furthermore, we study a certain explicitly-defined large family of matching field polytopes and prove that all polytopes in this family are connected by combinatorial mutations. Finally, we apply our methods to explicitly compute toric degenerations of small Grassmannians and flag varieties and obtain new families of toric degenerations.