System security is an increasingly important design criterion for many embedded systems. These systems are often portable and more easily attacked than traditional desktop and server computing systems. Key requirements for system security include defenses against physical attacks and lightweight support in terms of area and power consumption. Our new approach to embedded system security focuses on the protection of application loading and secure application execution. During secure application loading, an encrypted application is transferred from on-board flash memory to external double data rate synchronous dynamic random access memory (DDR-SDRAM) via a microprocessor. Following application loading, the core-based security technique provides both confidentiality and authentication for data stored in a microprocessor's system memory. The benefits of our low overhead memory protection approaches are demonstrated using four applications implemented in a field-programmable gate array (FPGA) in an embedded system prototyping platform. Each application requires a collection of tasks with varying memory security requirements. The configurable security core implemented on-chip inside the FPGA with the microprocessor allows for different memory security policies for different application tasks. An average memory saving of 63% is achieved for the four applications versus a uniform security approach. The lightweight circuitry included to support application loading from flash memory adds about 10% FPGA area overhead to the processor-based system and main memory security hardware.