In the context of digitalization, globalization, and heightened competition in the logistics sector, supply chain integration plays a crucial role in the economic success of Clearing and Forwarding companies in Kenya. The performance of these companies is marked by unsatisfactory customer experiences, stemming from delayed port arrivals, intricate regulations, inefficient document processing, and compliance checks. Consequently, C&F firms’ performance is compromised, leading to revenue. This performance challenge may be linked to insufficient customer systems integration. This study aimed to assess how customer systems integration influences the organizational performance of C&F firms in Kenya. The study employed a cross-sectional research design and gathered primary data via structured questionnaires. The sample consisted of 298 employees from departments including operations, customer service, and finance. Descriptive statistics and structural equation modelling were conducted using SPSS and SPSS AMOS 29 for data analysis. The study found that that there are varying degrees of alignment and interaction between the surveyed C&F companies and their customers. Further, the study found that customer systems integration has positive and significant effect (Path coefficient = 0.686***, C.R = 5.078, P.value = <0.001). The study concludes that that customer systems integration has beneficial effects on organizational performance of C&F firms in Kenya. Thus, C&F firms should invest in CRM systems to enable effective customer systems integration. Such systems can centralize customer data, track interactions, and offer insights into customer preferences and behaviour.