The study investigated into the factors that affect the quality of Integrated Science teaching and learning in second cycle institutions in the Juaboso District in the Western Region of Ghana. A survey design was adopted for the study. Structured questionnaire was used to collect information from a sample of 158 students and 11 Integrated Science teachers. Descriptive and inferential statistics were used to analyse the data. The study revealed that the instructional strategies employed by Integrated Science teachers during teaching and learning of Integrated Science were not varied, teacher centred and not inquiry based. Instructional materials utilized during Integrated Science lessons were inadequate. Lack of funds, no motivation by government and no heat source were the major constraints to teacher’s use of instructional materials. An independent-sample t-test results showed a significant difference between mean response of students (M= 43.56, SD = 25.61), and teachers (M =5.67, SD = 2.65) on availability of Instructional materials for teaching and learning Integrated Science (t (8.171) =4.415, p=0.002<0.05). Also significant difference exit between students and teachers mean response on the use of Instructional materials for teaching and learning Integrated Science; t (8.281) = 4.526, p=0.001<0.05. The Juaboso District Education Service in collaboration with the University of Education, Winneba should organize short courses on instructional strategies, material improvisation, production and utilization for teachers to improve the quality of Integrated Science teaching and learning in second cycle institutions in the Juaboso District.