The study explored the effect of bookkeeping on SME performance in Munuki Payam-Juba Central Equatoria State, South Sudan. The study adopted a descriptive cross-sectional design and a respondent of 99 owner managers of SMEs where considered. The study tested three null hypotheses: (i) Budgeting has no significant effect on SME performance in Munuki Payam-Juba Central Equatoria State, South Sudan, (ii) Tax compliance has no significant effect on SME performance in Munuki Payam-Juba Central Equatoria State, South Sudan, and (iii) Decision making has no significant effect on SME performance in Munuki Payam-Juba Central Equatoria State, South Sudan. The first null hypothesis was accepted, while both the second and third were rejected. The conclusion was made that bookkeeping significantly effects SME performance in Munuki Payam-Juba Central Equatoria State, South Sudan [F (1, 97) = 22.293, p < 0.05; R2 = 0.947]. Recommendations were given with regards to Owner manger training and government policy to enhance book keeping in order to improve SME performance. The study has attempted to respond to the call of Ahuja (2009) and Nyaga (2019) with regards to effect of book keeping in SME performance.