This paper provides evidence that the second language orthographic input affects the mental representations of L2 phonology in instructed beginner L2 learners. Previous research has shown that orthographic representations affect monolinguals’ performance in phonological awareness tasks; in instructed L2 learners such representations could also affect pronunciation. This study looked at the phonological representations of Chinese rimes in beginner learners of Chinese as a foreign language, using a phoneme counting task and a phoneme segmentation task. Results show that learners do not count or segment the main vowel in those syllables where it is not represented in the pinyin (romanisation) orthographic representations. It appears that the pinyin orthographic input is reinterpreted according to L1 phonology–orthography correspondences, and interacts with the phonological input in shaping the phonological representations of Chinese syllables in beginner learners. This explains previous findings that learners of Chinese do not pronounce the main vowel in these syllables.