The aim of our study was to determine the usefulness of mixtures of carvacrol and Bacillus thuringiensis crystalline proteins Cry against pests of two different species: Cydia pomonella L. (Lepidoptera: Tortricidae) and Spodoptera exigua Hübner (Lepidoptera: Noctuidae). The novelty of our work lies in showing the interactions between carvacrol and bacterial toxins against insect pests. Moreover, we have demonstrated that carvacrol applied via ingestion exerts toxicity against lepidopteran caterpillars. We have shown that the botanical compound and Cry proteins act in synergy and their mixtures are most effective in reducing the number of L1 and L3 larvae when B. thuringiensis toxins constitute up to 0.1% and 0.05% of the mixtures, respectively. Carvacrol and crystalline proteins act in synergy in these combinations and have the potential to be effective in protecting crops against lepidopteran pests. The nature of the interaction between the components depended on the proportion of their concentrations in the mixture. Mixtures containing Cry toxin concentrations equal or higher than 20% caused lower observed mortality of insects compared to the expected one. Furthermore, we showed that crystalline proteins of B. thuringiensis MPU B9, carvacrol and their mixture did not affect the morphology of insect haemocytes, and additionally, had no effect on the immune system.