The use of microprocessors in space missions implies that they should be protected against the effects of cosmic radiation. Commonly this objective has been achieved by applying modular redundancy techniques which provide good results in terms of reliability but increase significantly the number of used resources. Because of that, new protection techniques have appeared, trying to establish a trade-off between reliability and resource utilization. In this paper, we propose an application-based methodology, to protect a soft processor implemented in an SRAM-based FPGA, against the effect of soft errors. This is done creating a library of adaptive protection configurations, based on the profiling of the application. This hardware configuration library, combined with the reprogramming capabilities of the FPGA, helps to create an adaptive protection for each application. We propose two partial TMR configurations for the Arithmetic Logic Unit (ALU) as an example of this methodology. The proposed scheme has been tested in a RISC-V soft processor. A fault injection campaign has been performed to test its reliability.