The sustainability of control programs for the Mediterranean fruit fly, Ceratitis capitata, for citrus crops in Spain has been threatened by the development of resistance to malathion and lambda-cyhalothrin in recent years. Spinosad is widely used without apparent loss of efficacy. However, a highly resistant strain, JW-100s, has been obtained after laboratory selection. Spinosad resistance in JW-100s has been associated with different mutant alleles of the α6 subunit of the nicotinic acetylcholine receptor (Ccα6) including an isoform-specific truncation allele, Ccα6 3aQ68*. Using the GAL4 > UAS system in Drosophila melanogaster to demonstrate expression of this truncated α6 subunit, in a dα6 loss-of-function genetic background, does not rescue susceptibility to spinosad, while the expression of Ccα6 wild-type isoforms does. We have also generated C. capitata isolines from JW-100s homozygous for: (1) the Ccα6 3aQ68*Δ3b-4 allele, which contains the mutation 3aQ68*, and (2) the Ccα6 3aQ68*-K352* allele, which contains the mutations 3aQ68* and K352*. Neither of these produce complete Ccα6 transcripts. The frequency of resistant alleles declined when in competition with individuals carrying the wild-type allele. Through extensive testing of both biological and behavioral fitness traits, we identified a reduced ability of Ccα6 3aQ68*Δ3b-4 males to detect the parapheromone and to mate with females carrying the Ccα6 3aQ68*-K352* allele in competition experiments. Thus, not only the potential for spontaneous resistant mutations to arise in Ccα6 but also their fitness costs must be considered when planning resistance management strategies for C. capitata.