Irradiance variability is one of the main challenges for using photovoltaic energy. This variability affects the operation of maximum power point trackers (MPPT) causing energy losses. The logic of the Perturb-and-Observe MPPT algorithm is particularly sensitive to quick irradiance changes. We quantified the existing relation between irradiance variations and efficiency loss of the logic of the Perturb-and-Observe MPPT algorithm, along with the sensitivity of the MPPT to its control parameters. If the algorithm parameters are not tuned properly, its efficiency will drop to nearly 2%. Irradiance variability causes a systematic energy loss of the algorithm that can only be quantified by ignoring the hardware components. With this, we aim to improve the energy yield estimation by providing an additional efficiency loss to be considered in the calculations.