Antimicrobial coatings that are transparent and not easily stained are disclosed. Some variations provide a transparent antimicrobial structure comprising: a discrete solid structural phase comprising a solid structural polymer with a glass-transition temperature from 25° C. to 300° C.; a continuous transport phase interspersed within the discrete solid structural phase, wherein the continuous transport phase comprises a solid transport material; and an antimicrobial agent contained within the continuous transport phase, wherein the antimicrobial agent is dissolved in a fluid and/or in a solid solution with the continuous transport phase. The discrete solid structural phase and the continuous transport phase are separated by an average phase-separation length selected from 100 nanometers to 500 microns. This invention resolves the trade-off between antifouling and fluorinated material content. This invention also resolves the trade-off between transport of absorbed molecules and transparency. The result is an improved antimicrobial structure that is both antifouling and transparent.