In vitro biological neural networks (BNNs) provide well-defined model systems for constructively investigating how living cells interact with their environments to shape high-dimensional dynamics that can be used to generate coherent temporal outputs, such as those required for motor control. Here, we develop a real-time closed-loop BNN system that is capable of generating periodic and chaotic temporal signals by integrating cultured cortical neurons with microfluidic devices and high-density microelectrode arrays. We show that training a simple linear decoder with fixed feedback weights enables the system to learn and autonomously generate diverse temporal patterns. When feedback is switched on, the irregular activity in the BNNs is transformed into low-dimensional, structured dynamics, producing coherent trajectories that are characterized by stable transitions between different neural states. BNNs trained on various target frequencies—ranging from 4 to 30 s—can be trained to sustain oscillations at distinct frequencies, demonstrating their adaptability. Importantly, top–down control of the self-organized network formation with microfluidic devices is the key to suppressing excessive synchronization and increasing dynamic complexity in BNNs, facilitating the training process and the generation of robust outputs. This work offers a biologically inspired platform for understanding the physical basis of cortical computations and for advancing energy-efficient neuromorphic computing paradigms.