A port cap has a closed end, an open end, and a conical body made of a flexible material. An inside of the port cap may have a textured or uneven surface. The textured or uneven surface may be formed by one or more annular rings. An annular ring may be asymmetrical having different slopes on the two different sides of the annular ring. The port cap may be made of an elastomeric polymer or elastomeric copolymer. An insert inside the port cap may be made of a sponge or similar material and may contain a cleaning agent or microbiocidal. The port cap may be sealed with a lid. Methods of using the port cap are also disclosed.