Milk production of cows on farms in which milk was organically produced (OP) tends to be less than that on farms with conventional or integrated production (IP), but causes for the difference have not been thoroughly evaluated. We performed a study to investigate management, nutritional, metabolic, and endocrine risk factors that may be associated with lower milk production on OP farms. Fertility traits were also compared. In 60 OP and 60 IP farms, matched in size, location, and agricultural zone (altitude), 970 cows were selected. Body condition scores (BCS) and body weights (BW) were determined at approximately 29 d prepartum (visit 1) and at 31 (visit 2) and 102 d postpartum (visit 3). Blood was sampled at visit 2 to determine plasma concentrations of glucose, nonesterified fatty acids, β-hydroxybutyrate, albumin, urea, insulin-like growth factor-1 (IGF-I), and 3,5,3′-triiodothyronine. Metabolic and endocrine traits as well as milk yield, fertility, and feeding factors were compared among cows in the 2 production systems. A univariable and stepwise multivariable logistic regression model was used to identify risk factors for poor milk yield. Energy-corrected milk yield medians and milk urea concentrations were less in OP than in IP cows at visits 2 and 3. Organic farms provided less concentrates, and OP cows at all visits had lower BW than IP cows. Plasma albumin and urea concentrations were lower in OP than IP cows. The following factors were positively associated with low milk yield (below median): Simmental breed, greater BCS, positive California mastitis test in hindquarters, and sampling during summer. Factors associated with an elevated (above median) milk yield were: Holstein breed, greater BW and lactation number (age), weak udder suspension, greater blood albumin, milk fat and milk protein, more lactation persistency, longer calving intervals, routine teat dipping, and more outdoor access during winter. In conclusion, significant differences including milk yield were detected between Swiss OP and IP cows. Lower milk yields were due to a range of individual animal and farm-level factors such as breed, nutrition, management, and udder health.