Background: The association between the International Physical Activity Questionnaire Short Form (IPAQ-SF) and objective measures of physical activity has never been evaluated in participants with newly diagnosed bipolar disorder (BD). Our aim was to compare IPAQ-SF to objective measures in participants with newly diagnosed BD, their unaffected first-degree relatives (UR), and healthy control individuals (HC) in groups combined and stratified by group. Materials and methods: Physical activity measurements were collected on 20 participants with newly diagnosed BD, 20 of their UR, and 20 HC using individually calibrated combined acceleration and heart rate sensing (Actiheart) for seven days. IPAQ-SF was self-completed at baseline. Correlation between measurements from the two methods was examined with Spearman rank correlation coefficient and agreement levels examined with modified Bland–Altman plots. Results: Physical activity energy expenditure (PAEE) from IPAQ-SF was weakly but significantly positively correlated with physical activity estimates measured using acceleration and heart rate in groups combined (Actiheart PAEE) (ρ= 0.301, p = 0.02). Correlations for each group were positive, but only in UR were it statistically significant (BD: p = 0.18, UR: p = 0.007, HC: p = 0.84). Self-reported PAEE and moderate-intensity were markedly underestimated [PAEE in all participants combined: 62.7 (Actiheart) vs. 24.3 kJ/day/kg (IPAQ-SF), p < 0.001], while vigorous-intensity was overestimated. Bland–Altman plots indicated proportional bias. Conclusion: These results suggest that the use of the IPAQ-SF to monitor levels of physical activity in participants with newly diagnosed BD, in a psychiatric clinical setting, should be used with caution and consideration.