Abstract Integrating animals into a farm supports a closed or semi-closed production system where nutrients are recycled and off-farm inputs are reduced. In comparison to other livestock, chickens can be a low-investment option for animal-crop integration of small-scale, diversified, vegetable farms. Although crop-animal integration poses many potential benefits to farms, soils, and the environment, there are significant food safety risks when considering the production of vegetables in close proximity to raw manure. The objectives of this study were to examine the effects of poultry integration with meat chickens (broilers) in two different seasons on soil health, food safety, vegetable yield, and poultry feed efficiency in organic vegetable cropping systems. We explored these effects in an open field study with three rotation treatments (two that integrated chickens and a no-chicken control): vegetables-cover crop (V-CC; control treatment), vegetables-cover crop-poultry (V-CC-P), and vegetables-poultry-cover crop (V-P-CC). In response to crop rotation, over three years, we monitored soil nutrient status, soil microbial biomass carbon (MBC), permanganate oxidizable carbon (POXC), and microbial catabolic potential and diversity using Biolog® microplates. The presence or absence of foodborne pathogens in soil and vegetables was also measured. Nitrate–nitrogen (NO3–N) was higher in V-P-CC in year 2 as compared to both V-CC and V-CC-P (P = 0.001 and <0.001, respectively). After poultry removal in the summer of year 2 and year 3 V-P-CC was on average two times higher in NO3–N as compared to V-CC and V-CC-P, respectively. After chicken removal in the autumn of year 3 V-CC-P was 2.1 and 1.8 times higher in NO3–N as compared to V-CC and V-P-CC, respectively. On average phosphorus (P) increased by 45% in year 2 and by 13.2% in year 3. Microbial biomass carbon (MBC) increased from after harvest (summer) in year 1 to the end of the season (autumn) of year 2 from 219.75 to 303.23 mg carbon (C) kg−1. Integrating poultry increased MBC by 25%, on average between both treatments across all sampling dates, compared to the V-CC (P = 0.042). The vegetable-cover crop control (V-CC) preferentially used carbohydrates, compared to V-P-CC which corresponded to greater amino acid usage. Escherichia coli O157:H7 was detected in all plots in the spring of year 3 and select replications of plots in the autumn of year 3. Salmonella spp. was found in one plot in year 2. No pathogens were detected on the spinach crop when leaf surfaces were tested. Integrating chickens into organic vegetable crop rotations increases NO3–N and has the potential for off-farm fertilizer reductions if time and stocking density are further examined. However, poultry feed is often an off-farm input and should be considered when determining the true N input of this system. Soil health may be improved, but MBC and other soil health indicators should be monitored with longer-term rotations. There are food safety risks that come with the integration of chickens into vegetable production and fields should be treated as if raw manure has been applied. Despite the potential benefits of integrating poultry into vegetable crop rotations, more research on these systems is required to determine optimum integration strategies that provide maximum benefit to the producer, the animals, and the environment.