Forest ecosystems in Sri Lanka are under pressure from intensive human activity and climate change. Invasive species are one of the greatest threats to autochthonous species and ecosystems. In Bundala National Park of Sri Lanka, there are efforts to control and limit the spreading of unwanted invasive Prosopis juliflora (Sw.) DC. and Opuntia dillenii (Ker-Gawl.) Haw., which poses a significant risk to natural ecosystem conservation. Nine different treatment variants (four replications) were used to test which management approach provides the control of Prosopis juliflora. This research is based on nine repeated measurements from 2017 to 2021 on 36 permanent research plots (each 625 m2) with 27 observed plant species and a total of 90,651 recorded plant individuals. The results confirmed that the dynamics of species richness, heterogeneity, and evenness showed significant differences between treatments during the five years of dynamics. The lowest species diversity was found in the control variant, followed by treatments based on the hard pruning and thinning of Prosopis juliflora trees. In contrast, strategies emphasizing the complete uprooting of Prosopis juliflora trees, replanting, and support of the natural regeneration of native species showed high species diversity and a high overall number of plant species. Generally, treatments had a significant effect on species diversity and the number of individuals of Prosopis juliflora, while changes in the overall number of plant species were more affected by time and succession. Silvicultural treatments including pruning, uprooting, and thinning have proven to be essential tools for nature conservation across various sites, aimed at enhancing habitat diversity in the face of ongoing climate change.