The coffee berry borer (CBB, Hypothenemus hampei Ferrari, 1867) is a coffee pest causing significant economic losses worldwide. The ability of the insect to withstand coffee toxicity has been attributed to its gut microbiota. In this study, CBBs were collected from three organic coffee plantations with variable environmental conditions in Chiang Rai, characterized by evergreen, shaded and open plantations. This research aimed to assess the abundance and diversity of the CBB microbiota in three coffee plantations and the dominant or specific bacterial taxa in each habitat. The CBB gut microbiota profiles were also compared across the three plantations. Next-generation sequencing revealed that the microbiota profiles of the CBBs from the evergreen and shaded coffee plantations had similar species richness, with 23 operational taxonomic units (OTU) in each. The gut microbiome profile of the CBBs from the opened organic coffee plantation was less similar to the other two and had lower diversity, with only 10 OTUs. The most abundant species found in this study was Pseudomonas fulva (51%), followed by Achromobacter insolitus (19%) and Kluyvera cryocrescens (12%), which are important for caffeine degradation. Our results of the gut microbial community of CBBs provide valuable baseline data on organic coffee in northern Thailand that can be used for coffee pest and insect control in the future.