Micro and large-sized enterprises are important elements to enhance the economic growth of any country, and even more so for developing countries such as Mexico. These enterprises highly contribute to job generation, competitiveness, and gross domestic product, factors that are important for the developing of a nation. The aim of this paper is to study the impact of human capital investments in the efficiency of the 21 economic activity subsectors for micro and large-sized enterprises in the Mexican manufacturing industry between 2009–2021. The database come from Mexico Annual Manufacturing Industry Survey. Four Data Envelopment Analysis models are developed to study the relationship between annual average working days, annual average wages, and annual average investment in training with average sales per year. Data indicate that, most of the micro-sized enterprises of the Mexican manufacturing sector do not invest in human capital training, contrary to their large-sized enterprises. The results show that investing in human capital training increase sales and wages in micro-sized enterprises of the Mexican manufacturing industry, but it is not evident in large-size enterprises of the Mexican manufacturing industry. The calculation of the economic activity subsectors efficiencies using the developed Data Envelopment Analysis models indicate that all the economic activity subsectors with scale efficiency equal to one optimally invest, and the average amount of investments in human capital training needed to increase the global and pure technical efficiencies of the others are calculated with the developed Data Envelopment Analysis models. In the three main economic activity subsectors of the Mexican manufacturing industry, a significant increase—in 83.33% of cases—in wages and salaries is seen in both micro and large-sized enterprises. Particularly, the results indicate that the Chemical industry economic activity subsectors show the highest efficiency in both micro and large-sized enterprises when the human capital training variable is present. This paper demonstrates the importance of investing in human capital to enhance the efficiency of micro and large-sized enterprises.