Blossom and twig blight, caused by Monilinia spp., is the main disease in apricot trees. In this study, we installed transparent rain shelters in apricot orchards to study their influence on the modification of the microclimate at the level of the tree canopy and on the reduction in moniliosis damage in twigs. Rain shelters significantly reduced the leaf wetness time measured within the foliage compared to the unsheltered trees (a reduction of between 43% and 67%). However, very few differences were observed in the daily averaged air temperature (up to 6%) and daily averaged air relative humidity (up to 1%). In the first experiment, on the apricot variety Bergarouge® (CEP Innovation, Lyon, France), moniliosis damage on twigs in the absence of phytosanitary protection was reduced by up to 62% for the trees provided with rain protection compared to the trees that did not receive rain shelters. A second experiment, involving five apricot tree varieties, made it possible to verify that fungicide protection could be reduced for the trees protected by rain covers, reducing moniliosis damage on twigs compared to full fungicide protection combined without rain protection. Finally, a third experiment comprising two apricot tree varieties has shown that in organic orchards, rain protection provides protection against moniliosis (twig blight) that is equivalent to an organic farming fungicide protection programme based on the use of copper sulphate and calcium polysulphide.