Three different cotton production strategies [certified organic, conventionally grown, and reduced insecticide input/integrated pest management (IPM)] were compared in field-sized replicates in the Northern San Joaquin Valley (NSJV), California, from 1996 to 2001. We measured arthropod abundance, plant development, plant density, pesticide use, cost of production, lint quality and yields in the three treatments. Overall pest abundance was low, and a key cotton fruit pest, Lygus hesperus Knight, known as the western tarnished plant bug (WTPB), did not exceed action thresholds in any treatment. Organic fields had significantly more generalist insect predators than conventional fields during at least one seasonal interval in all but one year. While there were no significant differences in plant development, plant densities at harvest were lower in organic than conventional and IPM fields. Some measures of lint quality (color grade and bale leaf rating) were also lower in the organic treatment than in either the IPM or the conventional treatments. Synthetic insecticides, not allowed for use in organic production, were also used in significantly lower quantities in the IPM fields than in the conventional fields. Over the 6-year period of the study, IPM fields averaged 0.63 kg of active ingredient (AI) insecticide per hectare, as opposed to 1.02 kg AI ha−1 for conventional fields, a reduction of 38%. Costs of production per bale were on average 37% higher for organic than for conventional cotton. This cost differential was primarily due to greater hand-weeding costs and significantly lower yields in organic cotton, compared with either IPM or conventional cotton. Average 6-year yields were 4.4, 5.4 and 6.7 bales ha−1 for organic, IPM and conventional treatments, respectively. Low world cotton prices and the lack of premium prices for organic cotton are the primary obstacles for continued production in the NSJV.