The microbial deterioration of cultural heritage includes physical and chemical damage as well as aesthetic alteration. With the technological advancement, a plethora of techniques for removing unwanted microorganisms have opened up new opportunities for microbiologists and conservators. This article reviews the most applied, up-to-date, and sustainable techniques developed for the control of cultural heritage microbial deterioration presenting noteworthy case studies. These techniques include chemical methods, i.e., traditional biocides and nanoparticles; physical methods, such as mechanical removal, UV irradiation, gamma radiation, laser cleaning, heat shocking, microwaves, and dry ice treatment; and biological methods, such as natural molecules with biocidal activity, enzymes, and microorganisms. The application of control systems requires the comprehension of their behavior toward the unwanted microorganisms and possible interactions with the heritage materials. This overview shows also the control methods drawbacks for the purpose of creating awareness in selecting the most suitable technique or combination of techniques.