CpFTSY is a component of the chloroplast signal recognition particle (CpSRP) pathway that post-translationally targets light-harvesting complex proteins (LHCPs) to the photosynthetic (thylakoid) membranes in plants and green algae containing chloroplasts derived from primary endosymbiosis. In plants, CpFTSY also plays a major role in co-translational incorporating of chloroplast encoded subunits of photosynthetic complexes to the thylakoids. This role has not been demonstrated in green algae. So far, its function in organisms with chloroplasts derived from secondary endosymbiotic events has not been elucidated. Here, we report the generation and characterization of mutants lacking CpFTSY in the diatom Phaeodactylum tricornutum. We found that this protein is not involved in inserting LHCPs into thylakoid membranes, indicating that the post-translational part of the CpSRP pathway is not active in this group of microalgae, consistent with earlier reports. However, a strong decline of the PsaC subunit of PSI indicates a role for CpFTSY in the co-translational CpSRP pathway in diatoms. Its absence leads to a very similar phenotype as the one previously described for diatoms lacking CpSRP54. Both cpftsy and cpsrp54 mutants display an increased level of photoprotection, low electron transport rates, inefficient repair of PSII, reduced growth and an upregulation of proteins compensating for a non-functional co-translational CpSRP pathway during light stress conditions.