The anticipated emergence of quantum computers in the foreseeable future drives the cryptographic community to start considering cryptosystems, which are based on problems that remain intractable even with large-scale quantum computers. One example is the family of code-based cryptosystems that relies on the syndrome decoding problem. Recent work by Misoczki et al. (in: 2013 IEEE international symposium on information theory, pp 2069–2073, 2013. https://doi.org/10.1109/ISIT.2013.6620590 ) showed a variant of McEliece encryption which is based on quasi cyclic moderate density parity check (QC-MDPC) codes and has significantly smaller keys than the original McEliece encryption. It was followed by the newly proposed QC-MDPC-based cryptosystems CAKE (Barreto et al. in: IMA international conference on cryptography and coding, Springer, Berlin, pp 207–226, 2017) and Ouroboros (Deneuville et al. in Ouroboros: a simple, secure and efficient key exchange protocol based on coding theory, Springer, Cham, pp 18–34, 2017. https://doi.org/10.1007/978-3-319-59879-6_2 ). These motivate dedicated new software optimizations. This paper lists the cryptographic primitives that QC-MDPC cryptosystems commonly employ, studies their software optimizations on modern processors, and reports the achieved speedups. It also assesses methods for side channel protection of the implementations and their performance costs. These optimized primitives offer a useful toolbox that can be used, in various ways, by designers and implementers of QC-MDPC cryptosystems. Indeed, we applied our methods to generate a platform-specific additional implementation of “BIKE”—a QC-MDPC key encapsulation mechanism (KEM) proposal submitted to the NIST Post-Quantum Project (NIST:Post-Quantum Cryptography—call for proposals, https://csrc.nist.gov/Projects/Post-Quantum-Cryptography , 2017). This gave a $$5\times $$ speedup compared to the reference implementation.