Efficacious botanical derivatives can provide an alternative to synthetic pesticides for organic farming systems. However, there is lack of information regarding the side effects of organic pesticides on key soil ecological processes. In this study, we investigated the effects of aqueous extracts from Urginea maritima and Euphorbia myrsinites exhibiting translaminar and systemic activity against pests on microbial biomass and enzymatic activities in soil. Two grams of plant material was extracted with 100 ml of water and then diluted 1:100, 2:100, and 4:100 with distilled water. Diluted plant extracts were applied around hypocotyl of tomato by soil drench. The effect of both plant extracts on microbial biomass C, amount of total N and organic C, and enzymatic activity in soil was significant. After the last application, the highest microbial biomass C was determined in the lowest U. maritima concentration (U 1:100). Soils treated with the highest concentration of U. maritima (U 4:100) had always lower SMBC content than control soil. All concentrations of E. myrsinites decreased microbial biomass C by 18% to 27% compared to the control. Total nitrogen and organic carbon decreased in soils without (control) and with treated U. maritima extract from first application to last application. Phosphatase, urease, and beta-glucosidase activities were monitored in plant extract-treated soils. Except U. maritima 1:100 treatments of second and fourth applications, the other treatments of plant extracts negatively affected enzymatic activity in soil. U. maritima and E. myrsinites plant extracts exhibited different effects on soil microbial biomass and activity, probably because of their different chemical contents.