Systems and methods for exchanging and processing encoded quantum signals in quantum key distribution (QKD) systems in real time. A stream of quantum signals is sent from Alice to Bob. Alice only encodes sets or "frames" of the streamed quantum signals based on receiving a "ready" message from Bob. This allows for Bob to finish processing the previous frame of data by allowing different bit buffers to fill and then be used for data processing. This approach results in gaps in between frames wherein quantum signals in the stream are sent unencoded and ignored by Bob. However, those quantum signals that are encoded for the given frame are efficiently processed, which on the whole is better than missing encoded quantum signals because Bob is not ready to receive and process them.