Students must develop higher order cognitive skills (HOCS) that allow them to think critically and use their learning in novel situations. However, little is known about how including HOCS in teaching and assessment affects students’ perception of learning. We combine quantitative and qualitative data to determine whether the inclusion of HOCS and the presence of constructive alignment influences students' perceptions of learning within the first-year practical components of an undergraduate biology degree at a UK research intensive university. We applied the Blooming Biology Tool (BBT) and Bloom’s Dichotomous Key (BDK) to quantify the proportion of HOCS present during practical sessions and their related assessments and found that a combination of tools can be used to reliably assess the requisite cognitive skills required to complete tasks. Students completed an online survey and provided free-text responses regarding which practical sessions they perceived had the most beneficial effects on their learning. Students valued both LOCS and HOCS for their learning but could only recognise and value HOCS in practical sessions featuring high proportions of HOCS. Our research provides methods for assessing and improving constructive alignment in the teaching of biology and furthers our understanding of when students will recognise and value HOCS.