The objective of the research was to investigate Effects of Inquiry-Based Instruction on Acquisition of Process Skills, Interest and Performance in Ecology among Secondary School Students. Four objectives, research Questions and Hypotheses guided the research. The hypothesis were tested at p≤0.05 level of significance. Pretest and posttest, experimental and control group design was used for the study. The population comprised all 1908 senior secondary school Biology students in Lere zone. A sample consisting of 118 students randomly selected from two coeducational schools in Lere Education Zone was used for the study. The experimental group was taught Ecology concepts using Inquiry-based method while the control group was exposed to lecture method. Three validated instruments called Student Process Skills Acquisition Test (SPSAT), with r=0.74,Ecology Performance Test (EPT) with r=0.76and Students Ecology Concept Interest Questionnaire (SECIQ) with r=0.84 were used to gather data. Data collected were analyzed using t-test and Kruskal-wallis statistics. The results of the study revealed that differences exist on acquisition of process skills when students are exposed to inquiry and lecture teaching method in favour of experimental group.Statistics revealed that significant difference exist in the interest shown by SSS Students when they are exposed to inquiry and lecture teaching method in favor of experimental group. Based on the findings the following recommendations were made; the use of inquiry-based instruction should be encourage among teachers of ecology to improve student?s acquisition of process skills and Inquiry-based instruction should also be encouraged to promote the learning of Biology by both male and female students.