The opportunity for the smallholder beef farming system to support the growth of South Africa’s livestock industry is untapped. Slow growth of the sector is attributed to many limitations that affect the smallholder beef farming sector. The objectives of the current study were to identify and characterize the systemic challenges and constraints that confront market-oriented smallholder beef farmers in the Limpopo Province, South Africa. Data collection involved interviewing all the 62 farmers under the Limpopo Industrial Development Corporation (IDC)-Nguni project using structured questionnaires. The sample was predominantly males (87%) and adults aged over 45 years (88%). Close to half (47%) of the respondents had tertiary education. Major ecological and production challenges reported as percentages of respondents were drought (96%), rangeland degradation (94%), diseases (89%), feed shortage (86%), and inadequate water (82%). Nearly 50% of the respondents ranked the extent of these challenges as high to very high. Results indicated that poor access to finance, lack of infrastructure, and poor access to markets were some of the key limitations reported by more than 80% of the respondents with above 50% ranking them as high to very high. Logistic regression models showed that respondents’ perceptions to the majority of the challenges were largely influenced (p < 0.05) by education, access to formal training, farm size, and age. Given all the limitations found, current findings point to the prospects of designing strategies that support knowledge flows and capacitating the farmers with skills to combat the challenges.