This paper aims to describe the results of a research experiment conducted to aid in the design of an experimental didactic prototype for the teaching of organic matter decomposition through composting and to identify the general characteristics of the prototype that could be applied universally to experimental didactic prototypes for the teaching of the scientific skills of observation and classification. 120 3rd and 4th grade students from Manuelita Saenz school of basic education participated in this research process. The objective of this research was to design and build an experimental prototype of organic matter decomposition from the characterization of the scientific skills of observation and classification of the group of students. With regard to quantitative development, exploratory and descriptive processes in three stages were used. The first consisted of diagnosing the scientific skills of observation and classification and the level of understanding of the composting process among the subjects. The second involved the design and construction of the experimental prototype. The third involved an investigative approach on the relevant disciplinary subject to aid the design of a didactic guide. The characterization of the scientific skills of students under grades 3 and 4 indicates they were ranked on a low-performance level showing difficulties regarding the understanding of the decomposition process of the organic matter or composting. In this same line, the research findings confirm the initial approaches of this paper concerning the scientific approaches in elementary basic education through the inquiry-based science education and the use of experimental prototypes in order to improve the understanding of natural phenomena.