The Malay language has a transparent morphological system and, unlike English, it is written in a very shallow alphabetic-syllabic script. We predicted that beginner spellers (six-to eight-year-olds) of this Rumi script would encode words at the level of the syllable and morpheme, rather than the phoneme. Using the results of a 75-item spelling test, we grouped children (N = 97) into three stages of spelling proficiency, and analyzed their errors on subsets of stem words (n = 15 CV-CVC lexemes) and affixed words (n = 10 prefix + stem + suffix). The data show a developmental progression in the use of meta-linguistic awareness that does not include untutored phoneme-grapheme correspondences: Stage 1 children were more likely to preserve stem syllables (CVs) and affixes than single phonemes; Stage 2 spellers were able to combine CV units; and Stage 3 children, the most proficient group, spelled almost all prefixes and affixes correctly even when the target was a low familiarity word. Even though Rumi is more predictable than English at the phoneme-grapheme level, Malay children's early spellings are based on their knowledge of syllables and morphemes, large-size units that are reinforced in the classroom.