The objective of this study was to evaluate the effectiveness of ultrasonic waves in extracting phenolic, antioxidant, and antimicrobial compounds from the leaves, roots, and fruits of capers using aqueous solvents. To optimize two extraction parameters—time (10, 25, or 40 min) and ultrasonic intensity (40%, 70%, and 100%)—we employed response surface methodology and a Box-Behnken design. The optimal extraction conditions for maximizing the antioxidant and antibacterial compounds were determined to be 36 min with an ultrasonic intensity of 91%. Under these conditions, the total phenolic content of the extracts was found to be 21.80 mg/g for leaves, 14.96 mg/g for roots, and 15.11 mg/g for fruits. The IC50 values, which indicate the concentration required to scavenge 50% of DPPH free radicals, were 11.75 µg/ml for leaf extracts, 52.17 µg/ml for root extracts, and 50.97 µg/ml for fruit extracts. Regarding antibacterial activity, the Minimal Bactericidal Concentration (MBC) for leaf, root, and fruit extracts against Bacillus cereus were 2.82 mg/ml, 32.86 mg/ml, and 25 mg/ml, respectively. For Pseudomonas aeruginosa, the MBC varied: leaves were effective at concentrations ranging from 50 to 100 mg/ml, while root and fruit extracts required ≥ 100 mg/ml for inhibition. Overall, the findings demonstrated that increasing extraction time and ultrasonic intensity enhanced the extraction of antioxidant and antimicrobial compounds from caper leaves, roots, and fruits. Additionally, the aqueous extracts of capers exhibited an inhibitory effect on the growth of B. cereus and P. aeruginosa.