Traditional medicinal plants have attracted scientific interest due to their bioactive compounds, and the levels of their constituents vary with location and altitude. The present study was designed to evaluate the pharmacological potential of two traditional medicinal plants, Mikania micrantha and Ageratum huostonianum; these were collected from two sites, Murlen National Park (MNP) and Dampa Tiger Reserve (DTR), which are located at different altitudes. Both plant species are used by local traditional healers in Mizoram, Northeast India, for the treatment of various health problems. We hypothesized that altitudinal variation would affect these plants' chemical composition and bioactive potential. Plant extracts were evaluated for antioxidant, antimicrobial, and cytotoxic activities. The results show that the plants located at a higher altitude, i.e., MNP, showed higher TPC (615.7 ± 0.58 and 453.80 ± 0.95 µg gallic acid equivalents/mg of plant extract dry weight (µg GAE/mg) for M. micrantha and A. huostonium, respectively) and TFC (135.4 ± 0.46 and 120.66 ± 1.93 µg quercetin equivalents/mg of plant extract dry weight (µg GE/mg) for M. micrantha and A. huostonium, respectively). The extract of A. houstonianum (MNP) exhibited significantly greater antioxidant activity against ABTS radicals (IC50 241.6 µg/mL) as compared to the extract of A. houstonianum (DTR) (IC50 371.2 µg/mL). The composition of the bioactive compounds present in the plants was determined using UPLC-ESI MS/MS and GC/MS, which detected five and ten compounds in the A. houstonianum and M. micrantha extracts, respectively. Plant species collected from the Murlen National Park site had high bioactivity potential and contained several bioactive compounds. A distinct variation between the volatile and non-volatile compounds was revealed. The collective data in this study show the influence of altitude on the biological compound production of selected medicinal plants. The findings will be utilized in determining the plant material needed for the development of bioactive formulations.