Students, parents, and teachers in Indonesia get the tremendous effects of the coronavirus (Covid-19 Pandemic) when schools are closed and the rules of Large-Scale Social Restrictions (LSSR) were set to overcome the global pandemic. While the government is doing its best to handle the outbreak of the epidemic, teachers respond and strive to provide qualified education for their students during these difficult times. Sciences should be learned through minds-on and hands-on, hence teachers must be able to create virtual classroom conditions that help students maintain learning momentum while they cannot interact each other physically. This study aimed to identify the difficulties experienced by science teachers during online learning and describe the efforts of science teachers to conduct online learning during the Covid-19 pandemic. The research data were obtained through a survey using a semi-structured online questionnaire. The respondents were 82 junior high school teachers and 104 biology high school teachers in Indonesia. Data analysis used a quantitative descriptive approach. The results showed that the majority of science teachers (77.5%) got difficulty in managing online learning. This difficulty was identified in three main factors namely technology, students, and teachers. Internet access was a technological factor that causes the greatest difficulty (42.4%) in online learning. Other difficulties came from the students by 21.5%, including low motivation, time management skills that were not optimal, and the lack of communication devices such as smartphones. The third factor, namely teachers, contributed 36.1% of difficulties, especially related to the explanation of concepts and the use of online learning applications. Based on these difficulties, 77.4% of teachers made an effort to carry out online learning optimally by presenting the material and providing slide presentation, discussion, as well as learning evaluation. A small percentage of teachers (22.6%) used online classes only for task assignments and learning evaluation. The efforts of science teachers to manage online learning have not optimized students’ varied learning experiences because science can’t be learned by reading and discussion only, but also by hands-on activities.