This study assesses profitability and the factors influencing the use of certified common bean seeds in Mbozi and Momba districts of Tanzania. The study was motivated by the limited empirical evidence distinguishing the economic performance of certified seeds from uncertified improved and local landrace varieties, despite ongoing efforts to enhance seed system performance in sub-Saharan Africa. A sample of 340 smallholder farmers was selected using a simple random sampling method. A mixed-methods approach, integrating both quantitative and qualitative research techniques was used to analyse production costs, yields and profitability alongside gathering farmers’ perspectives on the use of certified common bean seeds. Gross margin analysis was applied to estimate the profitability of certified seed users, while binary logistic regression was used to identify the key factors influencing certified seed adoption. Results show that farmers using certified common bean seeds achieved significantly higher yields (619.98 kg/acre) and gross margins (TZS 670,347.61/acre)—approximately 2.6 times greater than those using uncertified seeds (330.83 kg/acre). Adoption was significantly influenced by membership in farmers’ groups, participation in production training, awareness of seed availability, income diversification, and productivity. The study advances existing research by providing disaggregated evidence on certified versus uncertified seed profitability—an aspect rarely addressed in Tanzanian seed system studies. The findings highlight that promoting certified seed use can substantially improve smallholder profitability, enhance agricultural productivity, and contribute to achieving Sustainable Development Goal (SDG) 2.3 on doubling smallholder productivity and income.