Background: Experimental/correlational studies have consistently demonstrated that the contents of an individual's goals play an important role within future motivations, learning processes, and outcomes. Aims: The aim of the study was to extend past findings by employing a three-point, cross-lagged latent simultaneous structural model in the examination of the role of intrinsic/extrinsic goals' effects on key proximal motivations, learning variables, and achievement in the context of a Japanese university. Sample: This study consisted of first-year students within seven departments, attending one university (n = 584). Methods: Employing three data points, separated by 8 and 7 months, this study tests the effects of students' instrumental goals on future motivations, approaches to learning and learning outcomes. Three goals were the focus of this study: Distal internally regulated, distal externally regulated, and proximal externally regulated. Internally regulated goals were hypothesized to be broadly adaptive, while externally regulated goals were hypothesized to be maladaptive. Results: Findings reflected the broad importance of internal regulation for goals. Internally regulated goals positively predicted mastery goals and negatively predicted task valuation and effort belief deficits 8 months later. While not predicting achievement directly, internally regulated goals were the strongest predictor of future deep approaches to learning despite the lag of 15 months. Proximal externally regulated goals had no significant cross-lagged effects, and distal externally regulated goals had a negative predictive effect on future deep approaches to learning. Conclusions: This study extends intrinsic/extrinsic goal research both within education broadly and in the context of Japan. Furthermore, instrumental goals were found to play important roles supporting students in overcoming future motivation deficits and the pursuit of deep approaches to learning.