In the field of communication, autoencoder (AE) refers to a system that replaces parts of the traditional transmitter and receiver with artificial neural networks (ANNs). To meet the system performance requirements, it is necessary for the AE to adapt to the changing wireless-channel conditions at runtime. Thus, online fine-tuning in the form of ANN-retraining is of great importance. Many algorithms on the ANN layer are developed to improve the AE’s performance at the communication layer. Yet, the link of the system performance and the ANN topology to the hardware layer is not fully explored. In this paper, we analyze the relations between the design layers and present a hardware implementation of an AE-based demapper that enables fine-tuning to adapt to varying channel conditions. As a platform, we selected field-programmable gate arrays (FPGAs) which provide high flexibility and allow to satisfy the low-power and low-latency requirements of embedded communication systems. Furthermore, our cross-layer approach leverages the flexibility of FPGAs to dynamically adapt the degree of parallelism (DOP) to satisfy the system-level requirements and to ensure environmental adaptation. Our solution achieves 2000× higher throughput than a high-performance graphics processor unit (GPU), draws 5× less power than an embedded central processing unit (CPU) and is 5800× more energy efficient compared to an embedded GPU for small batch size. To the best of our knowledge, such a cross-layer design approach combined with FPGA implementation is unprecedented.