The control of the Mediterranean fruit fly (Medfly), Ceratitis capitata, in citrus orchards in Spain is mainly based in three insecticides (spinosad, lambda-cyhalothrin and deltamethrin) and the liberation of sterile males. However, Medfly control is compromised by the development of lambda-cyhalothrin resistance and the detection of spinosad-resistant alleles in field populations. We report here, for the first time, resistance to deltamethrin in populations collected in fields under different management strategies, including MagnetMed™ traps coated with this insecticide and/or spinosad and lambda-cyhalothrin used as bait sprays, and even in populations obtained from non-treated fields. Two deltamethrin-resistant strains (BP-delta and Rfg-delta) were generated from the descendants of some of the field populations that showed lower susceptibility to deltamethrin. Both strains showed low susceptibility to MagnetMed™ traps, moderate susceptibility to Ceratipack traps, and lacked cross-resistance to spinosad and lambda cyhalothrin. Our data suggest that deltamethrin resistance was mediated by P450 enzymes, since bioassays with synergists showed that PBO reverted resistance in a field population and the laboratory strains, whereas the effect of DEF and DEM was minor and no mutations were found in the VGSC gene. The inheritance of resistance for both strains was completely recessive, autosomic and did not fit the mortality expected for a recessive character under a monogenic or digenic model. We also found that deltamethrin resistance presented a fitness cost in terms of males’ weight, males’ and females’ longevity and lifetime fecundity, with a more pronounced effect in the BP-strain than in the Rfg-delta strain. Our results highlight the need to implement insecticide resistance management strategies to prevent control failures.