Data integrity is crucial for the performance and reliability analysis of photovoltaic (PV) systems, since actual in‐field measurements commonly exhibit invalid data caused by outages and component failures. The scope of this paper is to present a complete methodology for PV data processing and quality verification in order to ensure improved PV performance and reliability analyses. Data quality routines (DQRs) were developed to ensure data fidelity by detecting and reconstructing invalid data through a sequence of filtering stages and inference techniques. The obtained results verified that PV performance and reliability analyses are sensitive to the fidelity of data and, therefore, time series reconstruction should be handled appropriately. To mitigate the bias effects of 10% or less invalid data, the listwise deletion technique provided accurate results for performance analytics (exhibited a maximum absolute percentage error of 0.92%). When missing data rates exceed 10%, data inference techniques yield more accurate results. The evaluation of missing power measurements demonstrated that time series reconstruction by applying the Sandia PV Array Performance Model yielded the lowest error among the investigated data inference techniques for PV performance analysis, with an absolute percentage error less than 0.71%, even at 40% missing data rate levels. The verification of the routines was performed on historical datasets from two different locations (desert and steppe climates). The proposed methodology provides a set of standardized analytical procedures to ensure the validity of performance and reliability evaluations that are performed over the lifetime of PV systems.