Cognitive load has been shown to reduce both Evaluative Conditioning (EC) effects and CS-US pairing memory. This suggests the successful encoding of CS-US pairings is required for eliciting EC effects. However, an alternative account may be that cognitive load impairs the encoding of individual CS or US stimuli in the first place. We examined this possibility by manipulating the presence or absence of an auditory two-back task at learning, and by measuring the memory for both individual CS and US stimuli and for their pairings. Cognitive load reduced memory for CSs, USs, and CS-US pairings. Of importance, however, it disrupted EC even when the encoding of individual CSs and USs composing a pair was preserved. A mediation analysis also supported the assumption cognitive load reduces EC effects because it hampers the encoding of CS-US relations. This confirms the encoding of CS-US relation is a critical, yet non-efficient, contributor to EC.