<p>Microbial monitoring and antimicrobial control are critical for ensuring biosafety in diverse environments, including healthcare, industrial, and closed-loop systems such as space stations. Conventional colony counting and antimicrobial efficacy testing techniques are labor-intensive, time-consuming, and prone to human mistakes. Recent advancements driven by system engineering principles, including increased automation, sophisticated image analysis, machine learning, and artificial intelligence, have revolutionized colony counting, yielding faster, more accurate, and reproducible results. Concurrently, the development of novel antimicrobial surface technologies, including metal-oxide-based coatings, polymer nanomaterial composite thin films, offers a proactive engineering solution to mitigate contamination risks. The current review highlights advances in automated colony counting techniques and the development of advanced antimicrobial surface technology. Crucially, it explores the integration of these automated processes into the standardized evaluation of antimicrobial activity. The review concludes by addressing persistent challenges, identifying research gaps, and outlining a future outlook for integrated, engineered systems to ensure robust biosafety in critical environments.</p>