A large-scale use of the renewable energy in agriculture has become an optimal way to successfully deal with the issues of sustainability and climate change. Recently, the integration of solar panels on the roof of the green-house gave birth to a new crop production system called photovoltaic greenhouse. In this paper, we investigated the shading effect of the flexible photovoltaic panels, mounted on the green-house roof area in the checkerboard format, on the microclimate and the tomatoes yield during the summer and winter period. This study was undertaken in a two tomato canarian greenhouses, typical of the south Mediterranean region. The results of our study showed that the photovoltaic panels covering 40% roof area of the canary type greenhouse does not have a significant effect on the climatic parameters. Additionally, during the hot period, the photovoltaic panels reduced the temperature inside the greenhouse and sometimes falling in the optimum range for the tomatoes growth. Furthermore, this occupancy rate of the photovoltaic panels does not have a significant effect on the overall yield of tomatoes.