Background Negative energy balance during the transition period is a concern for both conventional and certified organic dairy systems. During early lactation, supplemental strategies are used to cope with nutrient deficiencies that are associated with impaired health, production, and reproduction. As organic certified dairies in the United States face restricted access to dietary supplements, the evaluation of products especially formulated for organic production is needed. Our objective was to assess the effect of supplementing 0.45 kg/d of an organic rumen-protected fat (RPF) on health, metabolic status, and productive and reproductive performance of organic certified Holstein cows from 1 to 150 days in milk (DIM). Two-hundred and two cows were enrolled in a randomized blocked controlled trial conducted from January to July, 2017 in a certified organic dairy located in Northern Colorado (USA). Two groups were randomly assigned to be individually supplemented with organic RPF (ORG; n = 100) or control pellets (CON; n = 102) once per day, in addition to the total mixed ration (TMR). Outcomes of interest included disease occurrence, culling, mortality, serum concentration of glucose and non-esterified fatty acids (NEFA), milk yield (kg/d) and milk components, resumption of cyclicity, time-to-first artificial insemination (AI), conception at first AI, and conception within 150 DIM. Results A significant effect for the inclusion of RPF was found in daily milk yield; RPF supplemented cows had greater milk yield (1.6 kg/d) compared to CON cows up to 150 DIM (P = 0.03). During grazing, multiparous (MP) ORG cows had greater milk yield compared to MP CON cows, whereas no effect was found in primiparous (PP) cows. Health outcomes, serum metabolite concentrations, and reproductive performance were not affected by the inclusion of RPF. Body condition loss was smaller in the ORG group up to 80 DIM; however, there was no effect on body condition during the grazing season and in the overall study period. Conclusions These results indicate that supplementation of RPF increased daily milk yield and prevented body condition loss during transition. However, RPF supplementation did not affect health, serum metabolite concentration, milk components, and reproductive outcomes.