Later in 1993 Kuzyakov continued his research at the Humboldt University of Berlin and the Leibniz Institute of Vegetable and Ornamental Crops.

Yakov has published more than 875 scientific papers,[7][8] indexed by Web of Science and Scopus databases which include: He developed new concepts of Priming effect,[11][12] Microbial hotspots and hot moments in soil,[13] Transformation of low-molecular organic compounds in soil, Rhizosphere dynamics and stationarity,[14] Root exudation and its localization, Visualization of enzyme activity in soil,[15] Competition between microorganisms and roots for nutrients,[16] Pedogenic carbonates,[17] Agropedogenesis,[18] Partitioning and quantification of CO2 sources,[19] Biochar stability [20] etc.

The concepts, ideas and methodical approaches developed by Yakov Kuzyakov group stimulated many research directions worldwide.

[22] He has conducted research in all climatic zones including cold deserts, tropical areas and in various ecosystems (agricultural lands, forests, mountains, pastures, etc).

[23][24][25] The collaboration includes the projects with other research groups from Europe (Germany, Italy, France, Denmark, Russia, UK), Asia (China, South Korea, Indonesia), North and South America (USA, Chile), Africa (Tanzania) and Australia.