We extend the notion of standard pairs to the context of monomial ideals in semigroup rings. Standard pairs can be used as a data structure to encode such monomial ideals, providing an alternative to generating sets that is well suited to computing intersections, decompositions, and multiplicities. We give algorithms to compute standard pairs from generating sets and vice versa and make all of our results effective. We assume that the underlying semigroup ring is positively graded, but not necessarily normal. The lack of normality is at the root of most challenges, subtleties, and innovations in this work.