Several factors have been linked to honeybee colonies' decline, but many inhive therapies have been frequently used and little is known about their effects on honeybees. This study is aimed at evaluating some biological, histological, and biochemical changes in honeybees (Apis mellifera L.) workers exposed during development to the antibiotic Flagyl (metronidazole), commonly used as nosemosis therapy, compared to the natural substance thymol. This work was conducted in early spring, and the medicated sugar syrup was administered by feeding it to the honeybee colonies. Results revealed a significant reduction in the mean worker brood area and honey yield in colonies that received flagyl compared to control and thymol colonies (P<0.05). The weight of newly emerged workers in control colonies tended to be heavier than those in medicated colonies, though the differences were statistically insignificant. The histological analysis of the midgut confirmed severe changes in the cell structure of bees that received flagyl during development. It induced clear alterations in the epithelial cells, peritrophic membrane, and muscular layer. A significant reduction in protein content, as well as a decline in basic digestive enzymatic activity, were accompanied by changes in the midgut tissue as a result of flagyl application. Overall, these results are valuable in highlighting the validity of midgut histology and enzyme activities as indicators for evaluating the toxicity of used inhive therapy.