Aims This study aimed to highlight the importance of compost from aromatic plants as a stunning source for several bio active compounds generated from their inhabited thermophilic bacteria. Some of the isolated compounds could have a potential role in the treatment of microbial infections. Methods and Results A total of forty different thermophilic bacteria were isolated from compost samples during their thermophilic stage. These isolates were tested for their antimicrobial capabilities against different Gram-positive and -negative bacteria using agar diffusion and double layer agar methods. The potential isolates were further identified based on morphological, biochemical and 16S rRNA gene sequencing methods. They were subjected to submerged state fermentation and the total crude metabolites were recovered using ethyl acetate (EtOAc) extraction. All bioactive metabolites were identified using liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). It was observed that 2 out of 40 isolates were remarkably active against Gram-positive bacteria. These isolates were genetically identified as Bacillus species and their different active metabolites were characterized in the EtOAc extracts using LC-HRMS. Conclusion Liquid chromatography coupled with high-resolution mass spectrometry analysis of EtOAc extracts revealed the presence of active metabolites that are responsible for antimicrobial activities. Significance and Impact of the Study To the best of our knowledge, this is the first time to identify bioactive antimicrobial metabolites from retrieved compost micro-organisms in Egypt. So, compost could be a beneficial area for research as a reliable and continuous natural source for different uncountable communities of bacteria.