A farm to fork approach was used to establish the prevalence and risk of microorganisms in a carbonated soft drinks factory in south eastern Nigeria. Raw materials, intermediate and finished products were collected from 19 microbiological control points in a processing environment and analysed using membrane filtration over a 12 month period. Yeasts and other heterotrophic bacteria increased during the rainy season but there was no significant difference (p>0.05) in the proliferation of organisms among the analysed months. Although, organisms were not detected in finished products, there was 100% prevalence for yeasts and bacteria in the processing areas with high sugar activity. No mould, Pseudomonas aeruginosa or Escherichia coli were isolated. Overall, a 5 by 5 risk matrix showed that heterotrophic bacteria, yeasts or mould had low risk of reaching undesirable numbers. In addition to the prevalence investigation carried out in the processing environment, 864 properly stored bottles of the same brand of carbonated soft drink in trade were purchased from different commercial locations over 12 months and screened. No yeasts mould or coliform bacteria were isolated from the sampling carried out. In conclusion, heterotrophic bacteria and yeasts thrive more on equipment than intermediate or finished products in the process environment studied and the risks of product spoilage or people getting ill was generally low and may remain so, if good manufacturing and proper after sales handling of the products are observed. Study highlights the need to focus on areas of high sugar activity, to control undesirable organisms and further work is required to establish how microorganisms survive and form biofilms on bottling equipment after sanitation.