This paper comprehensively explores the development of a standalone and compact microwave sensing system tailored for automated radio frequency (RF) scattered parameter acquisitions. Coupled with an emitting RF device (antenna, resonator, open waveguide), the system could be used for non-invasive monitoring of external matter or latent environmental variables. Central to this design is the integration of a NanoVNA and a Raspberry Pi Zero W platform, allowing easy recording of S-parameters (scattering parameters) in the range of the 50 kHz–4.4 GHz frequency band. Noteworthy features include dual recording modes, manual for on-demand acquisitions and automatic for scheduled data collection, powered seamlessly by a single battery source. Thanks to the flexibility of the system’s architecture, which embeds a Linux operating system, we can easily embed machine learning (ML) algorithms and predictive models for information detection. As a case study, the potential application of the integrated sensor system with an RF patch antenna is explored in the context of greenwood hydration detection within the field of smart agriculture. This innovative system enables non-invasive monitoring of wood hydration levels by analyzing scattering parameters (S-parameters). These S-parameters are then processed using ML techniques to automate the monitoring process, enabling real-time and predictive analysis of moisture levels.