This research aims to identify and evaluate the systemic factors which may be related to decrease in Grade 6 learner’s achievement in Mozambique between 2000 and 2007, looking for possible changes in Educational Effectiveness over that period. SACMEQ III learner results from Grade 6 Reading and Mathematics showed an overall mean decrease from 2000 to 2007. The main research question addressed in this study is: What are the systemic contextual factors associated with decrease in achievement in Reading and Mathematics between 2000 and 2007 in Mozambique? The conceptual framework underpinning this research presents the education system in terms of inputs, processes and outputs (Howie, 2002). Hierarchical Linear Models, based on trend design approach (Nilsen, & Gustafsson, 2014) was used to assess the variation in learner achievement decrease associated with changes in schools inputs and processes. The findings suggest that school-level factors linked to inputs and antecedents have a strong effect on the decrease in learner’s achievement, compared to the processes and practices. Moreover, learners’ background factors, specifically parent’s education and use of language of instruction at home, seem to be the crucial factors associated with learner achievement decrease. When school level variables related to parent’s education, use of language of instruction at home, are included in the model, the amount of variation accounted for, showed an increase (from 23.5 % to 37.7 %,). One can argue that the variation accounted for variables such as parents’ education, whilst use of language of instruction could be indicative of changes in learner’s intake composition between 2000 and 2007. Implications of these findings on the assumptions for large scale assessment studies in developing countries, such as Mozambique, are key issues. For instance, a question could be raised about the “trend” assumption of large scale assessment: To what extent can the trend level of achievement be measured where the learner’s intake composition is changing over the time? In the SACMEQ studies a stronger longitudinal design is needed to investigate how both school and intake factors influence achievement.