This paper presents a fault injection method for SEU (Single Event Upset) emulation in FPGAs based on loading at the programmable logic a configuration file with an erroneous bit. A "Xilinx Zynq®-7000 All Programmable SoC" device has been used to implement it, which combines a hard microprocessor (Processing System PS) with Programmable Logic (PL). The emulation tool is fully implemented on the Zynq chip, which means that neither additional external equipment nor PCB modifications are needed. Communications to external devices that slow down the configuration process are avoided, so a high fault-injection rate is achieved. Previous works consider including fault injection circuitry at the PL. This circuitry can be affected by a faulty configuration file, leading the device to an unrecoverable state, which is named as "injection side effects". In the method proposed in this paper the injection is implemented in the processing system of the Zynq device, making the injection system independent to the programmable logic and avoiding the previously mentioned effect. This method allows using complete bitstreams, partial bitstreams and one-frame bitstreams to inject faults. A comparison is done so as to find the most appropriate bitstream type.