Mining is an important sector of the Philippine economy, but it often results in negative impacts on biodiversity. To mitigate these impacts, it is crucial to assess biodiversity in mining areas and integrate conservation efforts into mining operations. As part of the national policy guidelines on biodiversity compliance for mining companies, this study has conducted a systematic review to examine the various biodiversity assessment methods, tools, sampling designs, diversity parameters, values, and indices used in the Philippines' mining sites. Search engines and research databases were utilized in identifying diversity assessment-related research. Based on the eligibility criteria, only 25 of the 100 papers downloaded and two project terminal reports were eligible and considered in the review. It was found that authors commonly used transect line and quadrat methods for floral studies and transect line, mist netting, point count, and opportunistic sampling for faunal studies. Species abundance, relative abundance, dominance, frequency, relative frequency, density, relative density, percent cover, and importance value were the most frequently assessed biodiversity parameters, whereas the Shannon-Wiener diversity index, Simpson index, species richness, and evenness were the most commonly used indices. Endemism, economic importance, invasiveness, and conservation status were additional factors evaluated. Overall, this review provides an overview of the various biodiversity assessment methods used in the country's mining areas and offers guidance for future assessments in other mining landscapes. The limited number of studies related to biodiversity assessment in mining areas in the Philippines over the last decade highlights the urgent need for more research in this field.