Swedish morphemes are classified as prosodically specified or prosodically unspecified, depending on lexical or phonological stress, respectively. Here, we investigate the allomorphy of the suffix -(i)sk, which indicates the distinction between lexical and phonological stress; if attached to a lexically stressed morpheme, it takes a non-syllabic form (-sk), whereas if attached to a phonologically stressed morpheme, an epenthetic vowel is inserted (-isk). Using mismatch negativity (MMN), we explored the neural processing of this allomorphy across lexically stressed and phonologically stressed morphemes. In an oddball paradigm, participants were occasionally presented with congruent and incongruent derivations, created by the suffix -(i)sk, within the repetitive presentation of their monomorphemic stems. The results indicated that the congruent derivation of the lexically stressed stem elicited a larger MMN than the incongruent sequences of the same stem and the derivational suffix, whereas after the phonologically stressed stem a non-significant tendency towards an opposite pattern was observed. We argue that the significant MMN response to the congruent derivation in the lexical stress condition is in line with lexical MMN, indicating a holistic processing of the sequence of lexically stressed stem and derivational suffix. The enhanced MMN response to the incongruent derivation in the phonological stress condition, on the other hand, is suggested to reflect combinatorial processing of the sequence of phonologically stressed stem and derivational suffix. These findings bring a new aspect to the dual-system approach to neural processing of morphologically complex words, namely the specification of word stress.