In the last years great effort was made by the scientific community to investigate the role of phytoplankton in contaminants stress responses and metabolism. However, biotransformation pathways remain underexplored in phytoplankton groups, such as diatoms, that play important ecological roles in natural environment and that are routinely used in biotechnological processes. The present study adopted a multi-omics approach to investigate diclofenac (DCF) physiological effects, transcriptional responses and metabolism in the marine diatom Phaeodactylum tricornutum with the aim of getting an insight on biotransformation pathways. DCF resulted in mild physiological effects on P. tricornutum but gene expression analysis indicated that multiple molecular functions and biological processes were altered during exposure. Transcriptomic analysis suggested increased nutrients and energy requirements possibly associated with the contaminant stress and detoxification metabolism. DCF bioconcentration factor (BCF) was low and varied between 3.9 and 2.7 L kg−1 depending on the exposure concentration. In total 6 DCF metabolites were detected of which 4′-Hydroxydiclofenac, a metabolite generally associated with Cytochrome P450 (CYP) enzymatic activity. Involvement of CYPs in biotransformation was suggested via indirect evidences. The five additional DCF metabolites detected presented high molecular weight. These metabolites were not previously described in the literature and were hypothesized to be generated via amino acid (or peptides) conjugation. Gene ontology analysis indicated that amino acid and peptide biosynthetic pathways were regulated upon DCF exposure supporting a possible correlation between organic contaminants detoxification responses and amino acid and protein metabolism in this diatom. Our findings provide mechanistic insights into contaminant detoxification and contribute to highlight the diversity of biotransformation pathways in phytoplankton.