There is a severe lack of information about molecular mechanisms of pesticide resistance in the rust-red flour beetle, a major pest destroying grains and flour across Nigeria, hindering evidence-based control. Here, we identified to the species level three populations of the red flour beetle from Kano, Nigeria, as Tribolium castaneum (Herbst 1797) and investigated the mechanism driving their insecticide resistance. The IRAC susceptibility bioassays established cypermethrin resistance, with LC50s of 4.35–5.46 mg/mL in the three populations, NNFM, R/Zaki and Yankaba. DDT and malathion resistance were observed in NNFM, with LC50s of 15.32 mg/mL and 3.71 mg/mL, respectively. High susceptibility was observed towards dichlorvos in all three populations with LC50s of 0.17–0.35 mg/mL. The synergist bioassay with piperonylbutoxide significantly restored cypermethrin susceptibility, with mortality increasing almost threefold, from 24.8% obtained with 1.5 mg/mL of cypermethrin to 63.3% in the synergised group (p = 0.013), suggesting a preeminent role of P450s. The two major knockdown resistance (kdr) mutations, T929I and L1014F, in the IIS4 and IIS6 fragments of the voltage-gated sodium channel were not detected in both cypermethrin-alive and cypermethrin-dead beetles, suggesting a lesser role of target-site insensitivity mechanisms. These findings highlight the need to explore alternative control tools for this pest and/or utilise synergists, such as piperonyl butoxide, as additional chemistries in pesticide formulations to improve their efficacy.