It is estimated the relationship between the investment in innovation activities, the results of innovation and productivity in Peruvian manufacturing firms, using the multi-equation model, called the CDM model, which studies the entire innovation process. The quantile regression approach was used, using data from the II National Survey of Innovation in the Manufacturing Industry 2015 in Peru. The findings were that technological innovation is associated with a 56% increase in productivity in the company. Finally, the quantile regression approach shows that the effect of technological innovation on the firm’s productivity is heterogeneous, increasing the effect on bigger firms. If investment in technological activities increases by 1%, then the labor productivity increases by 0.22% and the returns of innovation depend on the entrepreneurial position according the distribution of productivity.