We focused on assessing the antimicrobial effects of functional yoghurts supplemented with clove and probiotics. The formulation of aqueous clove extract (ACE) incorporated with probiotic yoghurt (Streptococcus thermophilus, Lactobacillus bulgaricus, and Lactococcus lactis) was optimised in terms of aqueous clove extract concentrations (2.5-7.5% v/v), fermentation temperature (32-42 °C), and total culture concentration (1.5-4.5% v/v). pH, titratable acidity, syneresis, water holding capacity, viscosity, springiness, color difference, lactic acid bacteria viability, and the antibacterial property of 17 runs were determined as responses using Box-Behnken design. The results indicate that elevated ACE concentration leads to a significant (p < 0.05) increase in titratable acidity, antibacterial effectiveness (against K. pneumoniae and P. aeruginosa), springiness, and color profile. Conversely, an elevated fermentation temperature significantly (p < 0.05) reduces pH and L. bulgaricus viability (log CFU/mL). Additionally, there is a significant (p < 0.05) decline in S. thermophilus and L. lactis viability (log CFU/mL) as well as springiness with an increased culture concentration. The optimal conditions identified are 7.5% (v/v) ACE concentration, a fermentation temperature of 36.6 °C (37 °C), and a total culture concentration of 4.5% (v/v), resulting in a 79% desirability score. The spectra of components were mainly obtained at wavelength of 3258 cm-1, 1636 cm-1 and 1075 cm-1 in Fourier transform infrared (FTIR) spectroscopy of optimized functional yoghurt. Where, 3258 cm-1 corresponds to the stretching vibration of O-H (hydroxyl) groups, 1636 cm-1 corresponds to the C=O (carbonyl) stretching vibration, and 1075 cm-1 corresponds to the C-O (ether or alcohol) stretching vibration.