Automated sample preparation has increasing importance in analytical laboratories. The sample clean-up by solid-phase extraction (SPE) is a common technique with multiple alternating steps of liquid handling and pressure application—often performed time-consuming in manual. The Positive Pressure Unit (PPU) enables a fully automated SPE parallel processing of 24 to 96 samples. Multiple samples can be processed in short time frames—the sample throughput is high. The heavy use can cause wear and pollution of the devices. To ensure constant high-quality results, quality checks are required to evaluate the device performance and to detect faults. Two measurement methods were developed. For checking the physical performance, the pressure is measured at 96 positions simultaneously using a special sensor adapter. An additional compound-oriented measurement method is used to determine the concentration, recovery rate and repeatability using SPE of 24 aqueous standard caffeine samples. The success of the caffeine extraction is verified using liquid chromatography with optical detection. The results—the caffeine concentration, the coefficients of variation, and the recovery rates—provide information about the current condition of the PPU. These two quality check measurement methods may support a fast troubleshooting and maintenance and will reduce the downtime.