This paper examines the challenges associated with the use of ETL and ELT processes within data processing systems. These processes are of pivotal significance in the realms of data integration and analysis. However, a number of challenges that necessitate a robust foundation in scientific and theoretical understanding accompanies the implementation of these processes. Purpose: to examine the challenges associated with the development of data processing systems, with a particular focus on the significant time input associated with configuration and optimization, and issues concerning data quality, scalability, and security. Results: a number of recommendations and solutions have been proposed for choosing between ETL and ELT, for the optimization of processes, and for insured data quality and security. Practical significance: new approaches have been developed to improve the efficiency of work with corporate data storage. Discussion: the necessity to optimize ETL and ELT processes, to improve data quality and security, and to make a justified choice of data storage architecture for effective information management is emphasized.