This paper explores the relationship between innovation and these two determinants in micro and small enterprises (MSEs) in the manufacturing industry in Indonesia, using secondary data. The key question in this research: is there evidence of the importance of DT and clustering for innovation capability in MSEs in Indonesia? The paper analyzes secondary data from Indonesia’s National Agency of Statistics and reviews key literature on innovation and digitalization in MSEs, and industrial cluster development in Indonesia. It is found that the number of industrial clusters of micro-, small-, and medium-sized enterprises (MSMEs) is concentrated on the island of Java, where more than 50% of the population is located, and is the most advanced region in economic development and industrialization in Indonesia. The majority of MSME clusters are in the food industry and woodworking industries. Only a very few of MSEs in the manufacturing industry use the Internet and do innovation. The type of innovation mostly is product innovation. Both relationships between MSEs doing innovation and MSEs using the internet and the total number of clusters are positive. But, statistically, only the relationship between the number of MSEs doing innovation and use of the internet is significant.