Three Bacillus thuringiensis strains were isolated from a specific habitat of tropical greenhouses located in the Botanical Garden of Adam Mickiewicz University in Poznań, Poland. The BG11, BG12 and BG15 strains harbour genes encoding a specific set of insecticidal proteins (cry1Ba, cry1Ia, cry2Ab, vip3Aa)—entirely different from those found in commercial isolates, currently used as bioinsecticides. Despite high genetic similarity of the new strains, each of them produces unique Cry1Ba toxin as a main component of the parasporal crystals. Moreover, the tested entomopathogens contain genetic determinants encoding two types of chitinolytic enzymes ChiA and ChiB. The tested strains display insecticidal activity against two distinct, economically important pest insects, Cydia pomonella L. (Lepidoptera: Tortricidae) and Spodoptera exigua Hübner (Lepidoptera: Noctuidae). However, BG12 and BG15 strains are significantly more active than BG11 towards both pests. The BG12 and BG15 strains can be considered as candidates for the production of new lepidopteran-active bioinsecticides with high potential to augment the existing biocontrol strategies.