We studied the emotions experienced by students during the last two years of compulsory secondary education (15 and 16 years old) when learning physics and chemistry. The objective of this piece of research was to establish different relationship between emotions felt by students and variables like the didactic methodology or the kind of science they are learning. We have collected data from different subject blocks such as those related to matter, energy and electricity or kinematics and dynamics, and they were processed and analysed in order to establish relationships by courses. The sample comprised 282 students. The results revealed that pupils mainly experience more positive emotions towards the content of chemistry than towards that of physics. There is also a decrease in the mean frequency of positive emotions such as joy as they pass from K-9 to K-10, and an increase in negative emotions such as boredom. The pupils who experienced positive emotions towards chemistry content related these to how the teacher taught the subject, rather than to the content itself. Negative emotions towards physics contents were linked to the exclusive use of the textbook, solving physics problems, or giving oral presentations.