The aim of this study was to investigate the antimicrobial activity of endophytes isolated from the root of Pelargonium sidoides DC., and to explore the antimicrobial interactions between endophytic fungi and the host plant. The hypothesis explored is that medicinal plants used as an anti-infective may not only rely on the properties of the medicinal plant alone but also on the residing endophytes within the botanical matrix. The study further aimed to isolate and identify secondary metabolites from the endophyte exhibiting promising antimicrobial activity. Fungal cultures were isolated from P. sidoides root material, and extracts were prepared and tested independently and in combination with the host plant to determine the interactions. Antimicrobial studies were undertaken using the minimum inhibitory concentration (MIC) assay against Gram-positive (Staphylococcus aureus ATCC 25923 and Enterococcus faecalis ATCC 29212) and Gram-negative (Escherichia coli ATCC 8739 and Pseudomonas aeruginosa ATCC 27853) bacteria. The bioactive compound was identified using High Performance Liquid Chromatography–Mass Spectrometry–Solid Phase Trapping–Nuclear Magnetic Resonance (HPLC–MS–SPT–NMR). The identification of the bioactive endophyte was undertaken by polymerase chain reaction (PCR) amplification and deoxyribonucleic acid (DNA) sequence analysis of the internally transcribed spacer regions and intervening 5.8S nrRNA gene and partial beta-tubulin gene. The crude extract from the fungal isolate Penicillium skrjabinii exhibited antimicrobial activity against S. aureus and E. coli at 0.03 and 0.09 mg/mL, respectively. Bioassay-guided isolation was carried out and the major compound, dibutyl phthalate (which is known to be produced by micro-organisms) was isolated from the most active fraction. A number of endophytes displayed a synergistic interaction with the host plant. This is the first study reporting P. skrjabinii as an endophyte that produces dibutyl phthalate and further provides insight to endophytic interactions with the host plant (Pelargonium sidoides root).