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Accuracy in facial emotion recognition has shown to vary with ovarian hormones, both in naturally cycling women, as well as in women taking oral contraceptives. It remains uncertain however, if specific – endogenous and exogenous – hormonal levels selectively impact recognition of certain basic emotions (or neutral faces) and if this relationship coincides with certain affective states. Therefore, we investigated 86 women under different hormonal conditions and compared their performance in an emotion recognition task as well as self-reported measures of affective states. Based on self-reported cycle days and ovulation testing, the participants have been split into groups of naturally cycling women during their early follicular phase (fNC, n = 30), naturally cycling women during their peri-ovulatory phase (oNC, n = 26), and women taking oral contraceptives (OC, n = 30). Participants were matched for age and did not differ in education or neuropsychological abilities. Self-reported anxiety and depressive affective state scores were similar across groups, but current affective state turned out to be significantly more negative in fNC women. Independent of negative affective state, fNC women showed a significantly higher negativity bias in recognizing neutral faces, resulting in a lower recognition accuracy of neutral faces compared to oNC and OC women. In the OC group only, negative affective state was associated with lower recognition accuracy and longer response times for neutral faces. Furthermore, there was a significant, positive association between disgust recognition accuracy and negative affective state in the fNC group. Low progesterone levels during the early follicular phase were linked to higher negative affective state, whereas in the peri-ovulatory phase they were linked to elevated positive affective state. Overall, previous findings regarding impaired emotion recognition during OC-use were not confirmed. Synthetic hormones did not show a correlation with emotion recognition performance and affective state. Considering the important role of emotion recognition in social communication, the elevated negativity bias in neutral face recognition found for fNC women may adversely impact social interactions in this hormonal phase.