According to uncertainty calculations, the values recorded by means of commercial monitoring systems are expected to be less accurate than those recorded by a system optimized for the measurement of electrical parameters. This study aims to verify if a larger expected uncertainty for commercial system actually turns into a larger spread of the measured values around the true value. Therefore, the behavior of the two monitoring systems has been investigated for both crystalline silicon and amorphous silicon photovoltaic arrays. First, a detailed uncertainty budget has been calculated for various photovoltaic indicators – energy, yield and performance ratio. Secondly, these expected uncertainties are compared to the measured values. Results show that the uncertainty level of the commercial system is much larger, e.g. the performance ratio of the crystalline silicon array is ±18.4% for the commercial system, with respect to ±5.6% for the optimized one. Three sources mainly contribute to the uncertainty: measurements of irradiance, current and voltage. When coming to the comparison of the measured values the difference is well below the stated one for voltage (<2%) and current (<5%) but larger for irradiance (>10%). In particular the irradiance measured with the commercial system is systematically smaller, therefore the performance ratio values calculated through the commercial system are always overestimated and often larger than 100%.