In this paper, we propose an approach for energy-aware FPGA-based query acceleration for databases on embedded devices. After the analysis of an incoming query, a query-specific hardware accelerator is generated on-the-fly and loaded on the FPGA for subsequent query execution using partial dynamic reconfiguration. For each SQL query operation, a pre-synthesized partial bitstream implementation exists in a module library. This library includes modules for all major SQL operations like restrictions, aggregations, as well as more complex operations such as join and sort. The implementation of this flexible FPGA-based query accelerator approach on the embedded low-energy system-on-chip (SoC) platform Xilinx Zynq shows SQL query processing speeds comparable to high-end database servers, however, at a much lower energy consumption. Indeed, provided experimental results give evidence that the proposed architecture may reduce the amount of consumed energy to just 5% of the energy needed of an in-memory database system running on an x86-based server at equal throughput for respective benchmarks.