Due to their ability to wipe out pathogens, botanical medicines have been historically used to effectively combat severe ailments throughout time immemorial. Furthermore, owing to the limitations of current medical approaches, investigators have begun looking into generating fresh formulations that have enhanced antioxidant and antimicrobial capabilities. These activities of combination generated from the fruit and seed of medicinal plants were collected in this investigation from different geographical areas for determining antioxidant and antimicrobial activity. One of the medicinal plants, i.e., Zanthoxylum armatum, belongs to the family Rutaceae and has medicinal values as mentioned in the literature. The objective of our study is to analyse the antimicrobial and antioxidant potential of formulations (fruits and seeds with different proportions) from district Bageshwar (location Shama Dura) against specific pathogens. In order to achieve the objective, fruits and seeds of Zanthoxylum armatum were examined through Fourier-transform infrared spectroscopy (FTIR) and estimated in vitro for their synergistic antibacterial potential against three pathogenic microorganisms: Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus using disc-diffusion assays. In addition, antioxidant activity was also performed using 2,2-diphenylpicrylhydrazyl (DPPH) and estimating its phenolic and total flavonoid content. The results of these studies showed that the maximum zone of inhibition was observed in formulation (40:60; 9–11 mm), whereas the least was observed in formulation (20:80; 3–4 mm) against different bacterial strains. In addition, the formulated samples of fruit and seed combinations may have shown higher antioxidant activity (86.37%), total phenolic (416.2 mg GAE/g) and total flavonoid (166.4 mg rutin/g) content. In contrast, FTIR was used to detect the presence of functional groups in the formulated fruit and seed of Zanthoxylum armatum. According to the aforesaid finding, the formulation shows strong antibacterial and antioxidant action without compromising cell viability.