Abstract The employment of behind‐the‐meter solar photovoltaic (PV) systems has gained increasing popularity in recent years as more individuals and organizations aim to reduce their reliance on conventional grid‐connected power sources and take advantage of the environmental and economic benefits of solar power. However, precisely estimating the potential output of PV systems is a challenging task, since most of the PV systems used in residential properties have been installed behind the meter. Consequently, electric power companies are limited to accessing only the recorded net electricity consumption. This article introduces an innovative approach to estimate behind‐the‐meter PV power generation within a large region, utilizing a limited representative subset. The proposed framework integrates Missforest, that is, a robust tool for missing data imputation, with a hybrid application of K‐Means, Pearson Correlation Coefficient, and Principal Component Analysis, for the precise selection of representative PV sites. Additionally, it leverages the Informer model, a cutting‐edge deep learning‐based time series model, to link the relationship between the PV power generation at representative sites and the total PV power output on the entire region. To conduct a case study, the power output of 367 PV sites and solar radiation measured at 105 weather stations in Taiwan were collected and analyzed. The application of this comprehensive methodology demonstrates a notable advancement in the estimation of “invisible” PV power generation in comparison to other established techniques.