Today, the demand for continuous monitoring of valuable or safety critical equipment is increasing in many industrial applications due to safety and economical requirements. Therefore, reliable in-situ measurement techniques are required for instance in Structural Health Monitoring (SHM) as well as process monitoring and control. Here, current challenges are related to the processing of sensor data with a high data rate and low latency. In particular, measurement and analyses of Acoustic Emission (AE) are widely used for passive, in-situ inspection. Advantages of AE are related to its sensitivity to different micro-mechanical mechanisms on the material level. However, online processing of AE waveforms is computationally demanding. The related equipment is typically bulky, expensive, and not well suited for permanent installation. The contribution of this paper is the development of a Field Programmable Gate Array (FPGA)-based measurement system using ZedBoard devlopment kit with Zynq-7000 system on chip for embedded implementation of suitable online processing algorithms. This platform comprises a dual-core Advanced Reduced Instruction Set Computer Machine (ARM) architecture running a Linux operating system and FPGA fabric. A FPGA-based hardware implementation of the discrete wavelet transform is realized to accelerate processing the AE measurements. Key features of the system are low cost, small form factor, and low energy consumption, which makes it suitable to serve as field-deployed measurement and control device. For verification of the functionality, a novel automatically realized adjustment of the working distance during pulsed laser ablation in liquids is established as an example. A sample rate of 5 MHz is achieved at 16 bit resolution.