This research developed a performance evaluation quality management system and investigated its effectiveness in achieving intended learning outcomes (ILOs) of college students in courses and improving them and also how this could affect their motivation to study the course. The researchers used quasi experimental design with two groups; experimental and control. Research sample consisted of (36) students divided into: control (18) and experimental group (18), kindergarten major, registered in comprehensive sciences course. We developed a questionnaire to evaluate achievement of ILOs of comprehensive sciences course and used Keller Motivation Scale (Keller, 2010) as well as the performance evaluation quality management system (designed using excel program). Results indicated a statistical significant difference between means scores of students at both experimental and control group of the posttest of the questionnaire favoring the experimental group. Results also showed a statistical significant difference between mean scores of both groups using Keller’s motivational scale favoring the experimental group. This indicated that activating students’ role evaluating achievement of intended learning outcomes increased their learning motivation. The system used led to a higher achievement level to the experimental group in knowledge and understanding, intellectual and professional and practical skills of learning outcomes. Both groups had a high achievement level in general/transfer learning outcomes. Results revealed that experimental group overcame the obstacles of achieving LOs, agreed on improving some of them and had a higher motivation level than the control. The research ended with a suggestion to reformulate learning outcomes of comprehensive sciences course as one of the core courses of kindergarten major and some suggestions for futhur research.