Educators are increasingly required to assist learners not simply with subject content, but with developing metacognitive skills for independent learning, interdisciplinary learning and lifelong learning. However, there is a dearth of research on how metacognitive processing interacts with other forms of processing in authentic, real-world learning environments. In light of this, this study concerned itself with furthering understanding of metacognition, cognition and its interactions with other forms of conscious thought processing within the real-world setting of a Self-Access Learning Centre (SALC) supporting independent learning at tertiary level in Japan. This study employed a Grounded Theory Methodology, based on a constructivist paradigm, to explore the various forms of processing that occur during independent learning. A sample of 47 students in a Japanese University undertook a range of independent learning tasks individually and/or as part of a group. Verbal protocol analysis, discourse analysis, audio and video recordings were used to record various forms of processing that emerged during the implementation of the tasks within this independent learning context. This data was then subjected to the rigorous process of constant comparison, through which codes were developed, and the categories of processing, the processing sequences and the interplay between thought processes during independent learning were elucidated. As an exploratory study, the findings cannot be considered widely applicable to larger, more diverse learner populations. The findings have added new knowledge to the fields of metacognition and independent learning by identifying the categories of processing that account for all conscious processing occuring during independent learning. The resultant grounded theory posits that different types of processing, namely, metacognitive, cognitive, affective, physical and off-task processing, interact to influence the learning experience in independent learning. Finally, it postulates that each type of processing is multi-dimensional and that the interactions within and between these processes and the learning experience are non-linear and complex.