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A large body of literature documents the sensitivity of pupil response to cognitive load (e.g., Krejtz et al. 2018) and emotional arousal (Bradley et al., 2008). Recent empirical evidence also showed that microsaccade characteristics and dynamics can be modulated by mental fatigue and cognitive load (e.g., Dalmaso et al. 2017). Very little is known about the sensitivity of microsaccadic characteristics to emotional arousal. The present paper demonstrates in a controlled experiment pupillary and microsaccadic responses to information processing during multi-attribute decision making under affective priming. Twenty-one psychology students were randomly assigned into three affective priming conditions (neutral, aversive, and erotic). Participants were tasked to make several discriminative decisions based on acquired cues. In line with the expectations, results showed microsaccadic rate inhibition and pupillary dilation depending on cognitive effort (number of acquired cues) prior to decision. These effects were moderated by affective priming. Aversive priming strengthened pupillary and microsaccadic response to information processing effort. In general, results suggest that pupillary response is more biased by affective priming than microsaccadic rate. The results are discussed in the light of neuropsychological mechanisms of pupillary and microsaccadic behavior generation.