In this work, we propose an efficient scheduler and intelligent memory manager known as AMMC (Advanced Multi-Core Memory Controller), which proficiently handles data movement and computational tasks. The proposed AMMC system improves performance by managing complex data transfers at run-time and scheduling multi-cores without the intervention of a control processor nor an operating system. AMMC has been coupled with a heterogeneous system that provides both general-purpose cores and application specific accelerators. The AMMC system is implemented and tested on a Xilinx ML505 evaluation FPGA board. The performance of the system is compared with a microprocessor based system that has been integrated with the Xilkernel operating system. Results show that the AMMC based multi-core system consumes 48% less hardware resources, 27.9% less on-chip power and achieves 6.8x of speed-up compared to the MicroBlaze-based multi-core system.