Stabat Mater is composed in Pärt's characteristic tintinnabuli style (which he has employed nearly exclusively since 1976) in which arpeggiations of a major or minor triad are combined with ascending or descending diatonic scales.

The text of the Stabat Mater consists of ten stanzas, in an AABCCB rhyme scheme and a syllabic meter of 887887.

As in several of Pärt's works, measure breaks are determined not by regular groupings of beats and stress, but rather by the words themselves.

On a large scale, Pärt frames the ten stanzas with a 108-measure introduction and coda nearly identical in structure and musical materials; the vocalists sing only the word "Amen".

Within these frames, Pärt divides the ten stanzas into four groups, separated by instrumental interludes of a vastly different musical character.