Imazapyr+imazapic ready mix is the main herbicide used to weed control in Clearfield® Rice System. The continuous use of high doses may increase their residual activity in the soil. The aim of this research was determine the sensitivity of cover crops and soybean in rotation with flooded rice to different levels of imazapyr+imazapic residues in the soil and its effect on soil microbiology. A field experiment was performed during the 2014/15 and 2015/16 seasons. In the first crop season, flooded rice was cultivated using herbicide rates in order to have levels of residue in the soil: 0, 140 (label dosage, equivalent to 73.5+24.5 g a.i. ha-1), 280, 560, 840 and 1,120 g ha-1. After crop harvest, during fall-winter, it was sown ryegrass, white clover and fallow (no soil cover); and in the followed season it was sown soybean in the same area (simulating rotation crop). At that occasion, soil samples were collected to perform soil microbiology analyses of acid phosphatase, β-glucosidase, fluorescein diacetate and urease activity. Growth characteristics on cover crops related to residue levels, and soybean development related to soil residue and cover crops used was evaluated. The results showed that the increase of imazapyr+imazapic doses caused a negative effect on the cover crops evaluated at 75 and 140 days after sowing, mainly at doses greater than twice the label dosage that also reduced the growth and yield of soybean. In general, the enzymes activity in soil decreased as the dose of the imazapyr+imazapic residue increased, showing lower microbiota activity to herbicides degradation.