The current study examined in depth the effects of suprasegmental-based instruction on the global (comprehensibility) and suprasegmental (word stress, rhythm, and intonation) development of Japanese learners of English as a foreign language (EFL). Students in the experimental group (n = 10) received a total of three hours of instruction over six weeks, while those in the control group (n = 10) were provided with meaning-oriented instruction without any focus on suprasegmentals. Speech samples elicited from read-aloud tasks were assessed via native-speaking listeners’ intuitive judgments and acoustic analyses. Overall, the pre-/post-test data showed significant gains in the overall comprehensibility, word stress, rhythm, and intonation of the experimental group in both trained and untrained lexical contexts. In particular, by virtue of explicitly addressing first language / second language linguistic differences, the instruction was able to help learners mark stressed syllables with longer and clearer vowels; reduce vowels in unstressed syllables; and use appropriate intonation patterns for yes/no and wh-questions. The findings provide empirical support for the value of suprasegmental-based instruction in phonological development, even with beginner-level EFL learners with a limited amount of second-language conversational experience.