Firms have realised that they cannot compete successfully in a marketplace without considering their customers. The impact of Supply Chain Innovative Practices (SCIPs) on customer retention in manufacturing SMEs is not well recognized. This paper aims to examine the extent to which manufacturing SMEs embrace SCIPs and their impact on customer retention. A simple random sampling technique and cross-sectional research design were used. Data were collected from 168 SME owners in Mwanza-Tanzania using a questionnaire survey to test the relevance of transactional cost theory in ascertaining the impact of SCIPs on customer retention. To determine the relationship between SCIPs and customer retention, Multiple Linear Regression was used. The study spotted e-supply chain, customisation, just in time, collaborative SC, reverse logistics, SC configurations, green supply chain, outsourcing and cross-docking as the most SCIPs adopted in manufacturing SMEs. The spotted SCIPs showed a positive link and significant impact on customer retention in Tanzania’s manufacturing SMEs. Only reverse logistics had a non-significant impact. SCIPs are important tools for customer retention. Therefore, all actors along the supply chain of manufacturing SMEs should aim at adopting SCIPs to improve performance, satisfy and retain customers. The study enriches the literature by documenting the role of SCIPs in customer retention in manufacturing SMEs.