Agrivoltaic (AV) systems integrate the production of agricultural crops and electric power on the same land area through the installation of solar panels several meters above the soil surface. It has been demonstrated that AV can increase land productivity and contribute to the expansion of renewable energy production. Its utilization is expected to affect crop production by altering microclimatic conditions but has so far hardly been investigated. The present study aimed to determine for the first time how changes in microclimatic conditions through AV affect selected agricultural crops within an organic crop rotation. For this purpose, an AV research plant was installed near Lake Constance in south-west Germany in 2016. A field experiment was established with four crops (celeriac, winter wheat, potato and grass-clover) cultivated both underneath the AV system and on an adjacent reference site without solar panels. Microclimatic parameters, crop development and harvestable yields were monitored in 2017 and 2018. Overall, an alteration in microclimatic conditions and crop production under AV was confirmed. Photosynthetic active radiation was on average reduced by about 30% under AV. During summertime, soil temperature was decreased under AV in both years. Furthermore, reduced soil moisture and air temperatures as well as an altered rain distribution have been found under AV. In both years, plant height of all crops was increased under AV. In 2017 and 2018, yield ranges of the crops cultivated under AV compared to the reference site were −19 to +3% for winter wheat, −20 to +11% for potato and −8 to −5% for grass-clover. In the hot, dry summer 2018, crop yields of winter wheat and potato were increased by AV by 2.7% and 11%, respectively. These findings show that yield reductions under AV are likely, but under hot and dry weather conditions, growing conditions can become favorable.