Protected areas aim to conserve nature by providing safe havens for biodiversity. However, protection from habitat loss, poaching and other threats, is not guaranteed without adequate investment in their management. Here, we examine the relationship between management effectiveness using the Management Effectiveness Tracking Tool (METT) and trends of 79 populations of mammals and birds in 12 Southeast Asian protected areas from Cambodia, Indonesia, Thailand and Vietnam. Despite the negative influence of corruption on species population change, we find evidence that adequate financial and human resourcing are important determinants in achieving good biodiversity outcomes. Management resourcing, national government transparency and body size collectively explain 29% of the variation in animal population trends in our model. Our paper contributes to a growing evidence base linking management resourcing shortfalls to declining biodiversity populations in protected areas. Our key findings are relevant to international funding agencies, governments and NGOs, to aid decision making around the allocation of conservation resources in Southeast Asia.