Megaselia scalaris (Diptera: Phoridae) is regarded as a medically important insect worldwide because it is the source of different myiasis diseases. Therefore, it should be controlled for human welfare and for economic reasons. Accordingly, the larvicidal activity of six plant essential oils was determined against M. scalaris and their impacts on proteins and isozymes were also estimated in whole body homogenate of the third larval instars. The tested essential oils were chamomile (Matricaria chamomilla), clove (Syzygium aromaticum), orange (Citrus sinensis), rosemary (Rosemarinus officinalis), spearmint (Mentha spicata) and sweet basil (Ocimum basilicum). Results exhibited that the clove oil had the highest larvicidal activity, LC 50 is 2.38 ml/100g media, whereas, chamomile oil was the least one, LC 50 is 5.37 ml/100g media. Significant concentration-mortality responses of the treated larvae were observed towards all tested oils. Concerning protein estimation, the control protein content was 12.80±2.68 mg/g tissue, and the oil application produced an elevation in total protein contents in treated larvae. This elevation was significant (p<0.05) with clove, orange and spearmint oils amounted to be 92.19, 70.31 and 57.58%, respectively, compared to that of the control larvae, but insignificant (p>0.05) with chamomile, rosemary and sweet basil oils. The electrophoretic study revealed that the maximum number of native protein bands was seven at approximately rate of flow ranging between 0.14 to 0.72 in the control and clove, orange, spearmint and sweet basil treatments. One newly formed protein band was observed in whole body homogenate of clove, orange, rosemary, spearmint and sweet basil treatments. The profiles of β-esterase, alcohol dehydrogenase and aldehyde oxidase showed the same patterns in both control and treated larvae. On the other hand, there was a reduction in the isozymes amount percent in the treated larvae as compared with the control values. The biochemical changes in native proteins and isozymes could be used as a biochemical indicator of toxic stress.