Up-to-date meta-databases are vital for the analysis of biological data. However,the current exponential increase in biological data leads to exponentially increasing meta-database sizes. Large-scale meta-database management is therefore an important challenge for production platforms providing services for biological data analysis. In particular, there is often a need either to run an analysis with a particular version of a meta-database, or to rerun an analysis with an updated meta-database. We present our GeStore approach for biological meta-database management. It provides efficient storage and runtime generation of specific meta-database versions, and efficient incremental updates for biological data analysis tools. The approach is transparent to the tools, and we provide a framework that makes it easy to integrate GeStore with biological data analysis frameworks. We present the GeStore system, an evaluation of the performance characteristics of the system, and an evaluation of the benefits for a biological data analysis workflow.