The study investigated ways in which portfolios are used by students and instructors in learning and assessment of science education programmes in undergraduate level in Tanzania. Findings revealed that instructors and students had negative perceptions towards the use of portfolio, although portfolios helped in improving students’ academic achievement and independent learning, and motivating students towards learning. The challenges observed were a result of institutional context in terms of resources, class size, and allocation of time. The study concluded that portfolios tie assessment practices to instruction, and provide students’ academic achievements. The study recommends for professional development of instructors in the Higher Education institutions on the basics of portfolios. Several possibilities for further research on the use of portfolios for students learning, and on the use of electronic portfolios are proposed.