Students who stall in the final stage of their degree rarely do so because they lack technical skill. More often, confidence erodes under sustained uncertainty, motivation shifts from intrinsic engagement to anxious compliance, and the demands of organizing months of research exceed what willpower alone can sustain. This study examines those emotional and motivational dynamics directly, treating research self-efficacy and intrinsic motivation not as background variables but as the affective-motivational core of thesis performance. Using partial least squares structural equation modeling (PLS-SEM) grounded in self-determination theory and social cognitive theory, we tested an integrative model with data from 396 undergraduate students actively completing theses at public and private universities in the northern region of Peru. Four enabling factors — methodological competencies, intrinsic motivation, tutorial support, and resources and conditions — were linked to thesis quality and process efficiency through two mediating mechanisms: research self-efficacy (the confidence to face methodological difficulty without retreating) and project management (the behavioral self-regulation that converts motivation into organized work). Resources and conditions showed the strongest associations in the model, with the largest effects on both project management (β = 0.533) and research self-efficacy (β = 0.418). Self-efficacy, in turn, was the primary predictor of thesis quality (β = 0.518), while project management and quality together drove process efficiency. The model explained 70.5% of variance in thesis quality and 81.4% in process efficiency. These pa