Our research aims to study the difference in resting-state during EEG and fMRI experimental conditions, each of which has its own peculiarities. Therefore, we conducted EEG and fMRI experiments very close in terms of conditions, during which 108 and 109 healthy participants, respectively, were recorded at rest for ten minutes. Subjective content of conscious during resting-state was assessed using the Amsterdam Resting-State Questionnaire (ARSQ) 2.0. To approve the 10-factor structure of the questionnaire in both groups we used the method of confirmatory factor analysis, the differences between groups were assessed using the Mann-Whitney U test. In general, it was found that responses towards the Amsterdam Resting-State Questionnaire 2.0. were similar in both groups. However, during resting-state the EEG group had larger scores for Comfort, Sleepiness and Visual Thought, while the fMRI group had larger scores for Health Concerns. The gender differences were similar in both groups for the dimension of Verbal Thoughts, which was significantly higher in females. Thus, our findings imply a substantial effect of the experimental environment difference for fMRI and EEG on subjective thoughts and feelings during resting-state experience, even when the experimental conditions are similar. That should be taken into account when planning a research experiment and analyzing data.