The following is a good article on cleaning the greenhouse prior to major production time. Information is from the New England Greenhouse Update http://www.negreenhouseupdate.info/index.php/updates
It is best to clean greenhouses as they become empty rather than to wait until just prior to the spring growing season. Cleaning early will eliminate over-wintering sites for pests and reduce populations for the next crop cycle. Greenhouse pests will overwinter in weeds and protected areas in unheated greenhouse, especially if the winter is unseasonably warm.
Remove leftover plants and debris and clean the floor of soil, organic matter and weeds. Clean areas around furnaces and along side walls where small weeds are usually found. Use weed barriers, repair tears in worn weed barriers and do not use stone on top. Stone will trap soil and moisture and create an ideal environment for weeds, diseases, insects and algae. It is also a good time to correct any drainage problems and low spots in greenhouses.
Next, disinfect the growing and plant handling areas, and irrigation system. There are several different types of disinfectants that are currently used in the greenhouse for plant pathogen and algae control including quaternary ammonium compounds (Green-Shield®, Physan 20®, and Triathlon®), hydrogen dioxide (ZeroTol®, Oxidate®), chlorine dioxide (Selectrocide), hydrogen peroxide plus peroxyacetic acid (ScaniDate) and sodium carbonate peroxydrate (Green Clean Pro®, TerraCyte®). All these products have different properties, so read and follow label directions. Chlorine bleach may be used for pots or flats, but is not approved for application to walls, benches or flooring. Alcohol is flammable and therefore not used as a general disinfectant. However, it is useful as a dip or swipe treatment to disinfect propagation tools. If possible, disinfectants should be used on a routine basis both as part of a pre-crop clean-up program and during the cropping cycle.
Organic growers have limited options for disinfectants. Oxidate® is the only material mentioned above that is currently listed by the Organic Material Review Institutes (OMRI), see www.omri.org. Ethyl or isopropyl alcohol is also allowed under the organic standards. Organic growers should always check with their certifying organization before using any material new in their farming practices.