Analytical ecogeochemistry is an evolving scientific field dedicated to the development of analytical methods and tools and their application to ecological questions. Traditional stable isotopic systems have been widely explored and have undergone continuous development during the last century. The variations of the isotopic composition of light elements (H, O, N, C, and S) have provided the foundation of stable isotope analysis followed by the analysis of traditional geochemical isotope tracers (e.g., Pb, Sr, Nd, Hf). Questions in a considerable diversity of scientific fields have been addressed, many of which can be assigned to the field of ecogeochemistry. Over the past 15 years, other stable isotopes (e.g., Li, Zn, Cu, Cl) have emerged gradually as novel tools for the investigation of scientific topics that arise in ecosystem research and have enabled novel discoveries and explorations. These systems are often referred to as non-traditional isotopes. The small isotopic differences of interest that are increasingly being addressed for a growing number of isotopic systems represent a challenge to the analytical scientist and push the limits of today's instruments constantly. This underlines the importance of a metrologically sound concept of analytical protocols and procedures and a solid foundation of data processing strategies and uncertainty considerations before these small isotopic variations can be interpreted in the context of applied ecosystem research. This review focuses on the development of isotope research in ecogeochemistry, the requirements for successful detection of small isotopic shifts, and highlights the most recent and innovative applications in the field.