Ephemeral cropping systems are characterized by frequent disturbances of ecological processes, which may compromise the conservation of plant and arthropod diversity and the ecosystem services they may provide. Conservation biological control practices include habitat manipulations that provide non-pest resources and selectively enhance natural enemies' effectiveness. This study, conducted in eight commercial fields of organically grown tomato, compared the effectiveness of sown flower strips with semi-natural margins in regulating natural enemy abundance, biocontrol, and crop damage. During repeated visits, the abundance of different arthropod groups was recorded. Crop surveys included measurement of aphid abundance, parasitism, and leaf and fruit damage from sap-sucking and lepidopteran pests. Semi-natural habitats were associated with higher vegetation diversity, but natural enemies were more strongly associated with sown strips during flowering. Sap-sucking pests were always recorded in higher abundance in flower strips, but crop damage in the plots adjacent to these strips was lower, suggesting that these strips may act as a trap-crop. The inclusion of floral supplements enhanced the parasitism rate of aphids in the crop, and reduced the rate of increase of lepidopteran-caused foliar damage with time. Early in the growing season, semi-natural strips showed significantly lower levels of crop damage and aphid counts, suggesting that these habitats may be important during early crop colonization by natural enemies. These results indicate that the inclusion of flower strips enhances the conservation of arthropod functional diversity in ephemeral crops, and that diverse mechanisms are important for controlling different pests. However, the efficacy of habitat manipulation is likely to be greater when it is complemented with the conservation of diverse semi-natural vegetation in the pre-existing field margin.