Fruit flies of the tribe Dacini (Tephritidae) include many agricultural pests, but also crucial pollinators of orchids and other plants. Surveys for Dacini fruit flies were conducted using methyl eugenol, cue lure, and zingerone as male attractants across Sabah, Borneo, Malaysia in 2018 and 2019, in habitats ranging from primary forest in highly protected Conservation Areas, selectively logged forest, secondary forest, and highly disturbed sites. Because 2019 was a mast year with mass fruiting, our surveys of that year collected more than 33,000 flies, compared to just more than 500 flies in 2018 – with similar trapping efforts. Our work adds 46 species to the 43 previously known from Borneo, bringing the total for the island to 89. Three new species are described: Bactrocera (Bactrocera) melanobivittata Doorenweerd, sp. nov., Dacus (Mellesis) danumensis Doorenweerd, sp. nov., and Zeugodacus (Zeugodacus) cataracta Doorenweerd, sp. nov. The new species are only found in conservation areas; B. melanobivittata is attracted to methyl eugenol and D. danumensis and Z. cataracta are attracted to zingerone. A discussion on how biogeographic affinities of the species in the checklist support a strong biogeographic boundary across Wallacea is provided, significant records are highlighted, and the relevance of these fly species for protecting agriculture as well as native ecosystems is discussed.