Insect exclusion cages are commonly used in agricultural and ecological studies to examine plant-insect interactions in a field setting while maintaining control over insect populations. However, these insect cages can unintentionally alter the climate inside of the cage and impact plant physiology, growth and yield as well as insect populations. This can subsequently affect interpretations of experimental results obtained from caged experiments. To address this concern, we measured meteorological variables in conjunction with soybean physiology, growth, and yield over a two-year period. In a 2011 field study in southern Wisconsin, we compared photosynthetic rates, leaf area index (LAI), soil environmental conditions, and various components of yield for plants grown inside and outside of an industry standard insect cage (Lumite 32×32 mesh). Inside of cages, several variables were higher (P<0.05) including surface (0–6cm) soil moisture (38%), stomatal conductance (42%), and total plant biomass (30%), while LAI was 20% lower (P<0.001) inside of the cages. During the 2012 growing season, we measured wind speed, wind gusts, solar radiation, air temperature and relative humidity inside of cages compared to open field conditions. We found that wind speed and solar radiation were 89% and 42% lower, respectively, and air temperature, relative humidity and vapor pressure deficit were not significantly affected. There was also a significant (P<0.0001) effect of the time of day on differences in wind speed and radiation between cages and open field plots. Our findings suggest that commonly used insect cages significantly alter the microclimate inside of the cage, and create a radiation regime in which the amount of direct and diffuse radiation received by plants is altered compared to the open field. Plant physiological processes and growth are affected by these environmental changes, adding a confounding factor when comparing caged to open field plants. Because the effects are likely a function of the type of cage, and mesh size and color, we recommend that future studies more thoroughly measure the microclimate for a variety of common cage types used in experiments.