Abstract: Existing computer based data acquisition systems are cumbersome, expensive and have limited mobility. Part of the problem is the lack of integration of different components of such systems. Recent advances in systems-on-a-chip technology allows for compactness and integration. Computer based data analysis and interpretation requires acquired data in a digital format. To design future handheld data acquisition system, one needs to capture signals and store them into a non-volatile digital memory device. When writing to a Flash memory, existing systems require a personal computer. A prerequisite to the design of future handheld data acquisition system is the development of a Flash memory controller that writes data directly to a Flash memory device, without using a personal computer. The aim of this study is to design an efficient Flash memory controller that writes temporary collected data to a detachable Flash device. To achieve this task without the need of a computer, systems-on-a-chip design technology will be used. We analyze two mechanisms, to store these signals into a secured digital card. The first approach uses single-block write and the second one is based on the multiple-block write. This study shows that the multiple-block write mechanism is more efficient in terms of the time it takes to store the temporary acquired signals into the secure digital card.