The article refers to an investigation into curricular integration (CI) strategies of computer simulations (CS), level of guidance and teacher mediation on the given tasks when using a CS, in the recognition and conceptual elaboration of the structure of the matter and alterations in the physical state at a microscopic level, in tasks with same degree of orientation and the perception of autonomy by students in the 5th grade. Quantitative and qualitative methods were used. Regarding curricular integration strategies, the class with the best results was the class in which the EXPLORA 1 strategy was applied. With regard to task guidance, the groups submitted to a moderate guidance degree were those who obtained the best learning results. In relations to mediation, the results of mediation are not independent of students' learning and the perception that the student' have about the autonomy and the time they have for the autonomous work. We conclude that autonomy with low guidance can be ineffective and the mediation with a lot of teacher intervention in the context of moderately guidance task can also reduce effectiveness.