Within the last years, new techniques for network covert channels arose, such as covert channel overlay networking, protocol switching covert channels, and adaptive covert channels. These techniques have in common that they rely on covert channel-internal control protocols (so called micro protocols) placed within the hidden bits of a covert channel’s payload. An adaptable approach for the engineering of such micro protocols is not available. This paper introduces a protocol engineering technique for micro protocols. We present a two-layer system comprising six steps to create a micro protocol design. The approach tries to combine different goals: (1) simplicity, (2) ensuring a standard-conform behaviour of the underlying protocol if the micro protocol is used within a binary protocol header, as well as we provide an optimization technique to (3) raise as little attention as possible. We apply a context-free and regular grammar to analyze the micro protocol’s behavior within the context of the underlying network protocol.