How can I store a binary file in a Kubernetes ConfigMap?

What I would do is encode this file in base64 and then the container that uses decoded to be able to use it

Binary ConfigMaps are now supported since Kubernetes version 1.10.0. From the readme notes:

ConfigMap objects now support binary data via a new binaryData field. When using kubectl create configmap --from-file, files containing non-UTF8 data will be placed in this new field in order to preserve the non-UTF8 data. Note that kubectl's --append-hash feature doesn't take binaryData into account. Use of this feature requires 1.10+ apiserver and kubelets. (#57938, @dims)

See the changelog for more details: https://github.com/kubernetes/kubernetes/blob/master/CHANGELOG/CHANGELOG-1.10.md#apps