Background: Owing to the importance of enzyme in fruit processing, demand in quality pectinase has increased. As a result, understanding the properties of locally produced pectinase is very important to encourage promotion in its application in the industry. In this study, Aspergillus niger was isolated, screened for its ability to secrete pectinase. The screened Aspergillus niger was used to produce pectinase using solid state fermentation of orange peels. Results: The effect of temperature and its stability, pH and its stability, substrate concentration, metal ions (Na+, Ca2+, Mg2+, K+, Mn2+, Zn2+, Co2+, and Fe2) were also investigated. The characterized pectinase was applied in the clarification of both orange and pineapple juices. The findings revealed that the enzyme was most effective at 50oC and relatively stable at 20oC activity of about 0.50 mg/ml for both. The optimal pH of 5 at about 0.50 mg/ml, and stabilized pH of 4 with approximately similar activity was also obtained. Of the metals ions investigated, Na+ gave the highest activity of about 0.61 mg/ml compared to ethylenediamine tetraacetic acid (EDTA) which displayed an inhibitory effect. On further optimizing for the concentration of Na+, low concentration of the ion (10 mM) had higher activity of about 0.61 mg/ml. The (Km) and Vmax was about 0.36 mg/ml and 4.39 U/ml. Conclusion: The characterized pectinase clarified both orange and pineapple juices, with enhanced clarification in orange juice compared to pineapple juice. Therefore, the characterized crude pectinase was suitable for application in the clarification of juices.