The demand for organized storage concepts to maintain, collect and distribute compounds has grown not only at pharmaceutical companies, but also at smaller research organizations and academic laboratories where there is the demand to store and retrieve substances systematically. However, budget limitations have prevented these smaller groups from buying costly storage systems offered by specialized commercial vendors. On the other hand, within pharmaceutical companies a need for inexpensive and flexible storage concepts has developed and complements the existing automated archives. For reasons of efficiency, most companies have built centralized facilities holding large collections of internal medicinal chemistry compounds to assist various, globally distributed research programs. This standardization and centralization though is not always ideal for a global organization. Therefore, site specific and localized requirements need to be addressed to ensure quick on site access to compounds without losing the global accessibility to them. In this article, we describe an approach towards a low cost and highly flexible store concept with manual compound stores of variable design addressing local needs, created to complement the existing automated stores. A key component of our implementation is the Compound Store Manager software which is capable of administering the different global stores. The developed backend system and centralized data management facilitates the operation and integration of the stores into an existing store environment.