This disclosure relates generally to field-programmable gate arrays (FPGAs). Some implementations relate to methods and systems for partitioning FPGA circuit designs to facilitate certification. In one aspect, a method includes generating a hardware description language (HDL) implementation of a circuit design. The method additionally includes partitioning the design into a first portion and a second portion. In some implementations, the second portion corresponds to a safety-critical portion of the design while the first portion corresponds to a non-safety-critical portion. The method additionally includes generating first configuration settings for the first portion and generating second configuration settings for the second portion. The method additionally includes verifying, or providing to a third-party certification body for verification, the first configuration settings for the first portion and the second configuration settings for the second portion. The method further includes providing the configuration settings for the second portion for programming into a PLD.