Crude, phenolic-rich extracts (CPREs) were isolated from different sources, such as Hibiscus sabdariffa (H. sabdariffa), Brassica oleracea var. capitata f. rubra (B. oleracea) and Beta vulgaris (B. vulgaris) and characterized. These CPREs showed potential antibacterial and antifungal activities. H. sabdariffa CPRE (HCPRE) is the most potent, as it inhibited all tested bacteria and fungi. Total anthocyanins content (TAC), total phenolic content (TPC) and total flavonoid content (TFC) were estimated in all three CPREs. H. sabdariffa contained 4.2 mg/100 g TAC, 2000 mg/100 g of TPC and 430 mg/100 g of TFC in a dry weight sample. GC–MS analysis of HCPRE showed 10 different active compounds that have antimicrobial effects against pathogenic bacteria and fungi, especially alcoholic compounds, triazine derivatives and esters. Scanning and transmission electron microscopy images of Staphylococcus aureus DSM 1104 and Klebsiella pneumonia ATCC 43816 treated with HCPRE (50 µg/mL) exhibited signs of asymmetric, wrinkled exterior surfaces, cell deformations and loss of cell shapes; and adherence of lysed cell content led to cell clumping, malformations, blisters, cell depressions and diminished cell numbers. This indicates death of bacterial cells and loss of cell contents. Aspergillus ochraceus EMCC516 (A. ochraceus, when treated with 100 µg/mL of HCPRE showed irregular cell organelles and cell vacuolation.