Morphological segmentability, i.e., the degree to which complex words can be decomposed into their morphological constituents, has been considered an important factor in research on morphological processing and is expected to affect acoustic duration (e.g., Hay 2003, 2001). One way of operationalizing segmentability is through the relative frequency of a complex word to its base word. However, relative frequency has failed to affect duration for different affix categories in many previous studies. One potential reason is the fact that complex words vary in their prosodic structure, depending on the prosodic integration of the affix (Plag & Ben Hedia 2018). In a large corpus study with three different corpora and eight affixes each, we investigate how prosodic word structure and relative frequency influence duration, and how these two factors interact. We find that prosodic structure does not significantly interact with relative frequency. Second, we show that relative frequency effects on duration do not emerge consistently across a large number of affixes. Third, not only does prosodic word structure not explain the absence of relative frequency effects, it also often cannot account for durational differences as such. We discuss these findings in light of phonological theory and speech production models.