This deposit contains data set and analytic codes (with a meta data) supporting "How do management decisions impact butterfly assemblages in smallholding oil palm plantations in Peninsular Malaysia?". We investigated the impacts of replanting and alternative replanting decisions (replanting with monoculture versus polyculture oil palm plantations) on within-plantation environmental conditions and butterfly assemblages (diversity, density, and composition). We also assessed the effects of habitat structure and complexity within plantations on butterfly assemblages. Funding and research permission: Jardine Foundation, the Cambridge Trust, and Tim Whitmore Fund provided funding for MFH, the Biotechnology and Biological Sciences Research Council (BBSRC) funded JS (USN: 304338625), and BBSRC (BB/T012366/1) provided funding for the establishment of the plots and surveys of environmental parameters. Research permission was provided by the Economic Planning Unit (EPU) of Malaysia’s Prime Minister’s Department for MFH (Ref: EPU 40/200/19/3727) and JS (Ref: MEA 40/200/19/3705).