Artificial insemination (AI) and selective bull mating are considered as robust methods for dairy cattle breeding. Globally, these methods have been used to enhance productivity and realize rapid genetic gains. However, these technologies have had low adoption rates in sub-Saharan Africa (SSA). Even though available evidence suggests that this is due to various infrastructural and technical challenges. There is limited information about what drives this low uptake of AI from a farmer’s perspective. Therefore, the main objective of this study was to determine and characterize factors that influence the choice by smallholder farmers between bull service and AI for dairy cow breeding. Further, the relationships between the breeding choices and the bio-physical elements of dairy farming, mainly, farmer characteristics, household income levels, farm management practices, and institutional support structures, were investigated. Data were collected through face-to-face interviews from a total of 16,308 small-scale dairy farmers in Ethiopia (n = 4679), Kenya (n = 5278), Tanzania (n = 3500), and Uganda (n = 2851). The questionnaire was coded in an electronic form using Open Data Kit (ODK) platform to allow for real-time data entry and management. Descriptive statistics, chi-square test, and a t-test were used to evaluate the independent and dependent variables, while logistic regression and factor analysis were used to identify factors that influenced farmers’ breeding decisions. Results showed that there was a significant difference in animal husbandry practices between farmers who used artificial insemination (AI) and those who practiced bull mating. The majority of farmers who used AI kept records, purchased more animal feeds, had more labor by hiring workers whose average wages were higher than those of bull service farmers. However, farmers who used AI pay more for services such as water access and breeding while their service providers had to cover long distances compared to farmers who used bulls. This indicates limited access to services and service providers for AI farmers. The ratio of AI to bull service users was even for Ethiopia and Kenya, while in Uganda and Tanzania, more farmers preferred bull service to AI. It was established that the factors that influence farmers’ breeding decision were not the same across the region. Factors such as farmer’s experience in dairy farming, influence of the neighbor, farmer’s ability to keep records, and management practices such as water provision and availability of feeds had a significant association (p < 0.001) with AI adoption among dairy farmers. In contrast, large herd and large land size negatively influenced AI adoption. Institutional settings including cost of AI service and the distance covered by the service provider negatively affected (p < 0.001) the choice of AI as a breeding option. There was a high probability of continued use of a specific breeding method when there was a previous conception success with that same method. Based on the results obtained, we recommend that improvement of institutional settings such as the availability of AI service providers, as well as better access to services such as water, animal feed, and animal health provision, be treated as critical components to focus on for enhanced AI adoption. Most importantly, there is a need to avail training opportunities to equip farmers with the necessary skills for best farm management practices such as record keeping, proper feeding, and selective breeding.