Over the past two decades, affective determinants of exercise behavior have received increasing attention in research on health promotion and prevention. To date, however, little is known about changes in affective exercise determinants during multi-week training programs in insufficiently active individuals. This applies in particular to the currently discussed advantages and disadvantages of high-intensity interval training (HIIT) compared with moderate-intensity continuous training (MICT) with regard to the affective experience of these two training types (e.g., reduced monotony vs. more aversive response during HIIT), which is important for exercise adherence. Referring to the Affect and Health Behavior Framework (AHBF), this within-subject study investigated changes in affective exercise determinants as a function of training type and sequence consisting of MICT and HIIT. Forty insufficiently active healthy adults (Mage = 27 ± 6 years; 72% women) underwent two 6-week training periods in a randomized sequence (MICT - HIIT vs. HIIT - MICT) within 15 weeks. Pre-post questionnaires and in-situ measurements, during and after a standardized vigorous-intensity continuous exercise session (VICE), were used to assess affective attitude, intrinsic motivation, in-task affective valence, as well as post-exercise enjoyment. These four affect-related constructs were collected before, between, and after the two training periods. Mixed models revealed a significant effect for training sequence (p = 0.011) - but not for training type (p = 0.045; non-significant after Bonferroni alpha adjustment) - on changes in in-task affective valence in favor of the MICT - HIIT sequence. Moreover, no significant training type or sequence effects were found for the constructs of reflective processing: exercise enjoyment, affective attitude, and intrinsic motivation. Therefore, individual-based training recommendations should consider the effects of variety and training sequence to develop tailored interventions that lead to more positive affective experiences - in particular during exercise - and promote the maintenance of exercise behavior in previously inactive individuals.