The aim of this study was to examine associations of body composition (fat mass index, % fat mass, fat-free mass index, body mass index) and physical fitness (cardiorespiratory fitness and handgrip strength) with gestational diabetes and cardiovascular health in early pregnancy. This cross-sectional study utilized baseline data (n = 303) collected in early pregnancy from the HealthyMoms trial. Body composition was measured using air-displacement plethysmography, cardiorespiratory fitness was assessed by means of the 6-min walk test and handgrip strength using a dynamometer. Logistic regression was used to estimate odds ratios (ORs) for gestational diabetes as well as high (defined as 1 SD above the mean) blood pressure, homeostatic model assessment for insulin resistance (HOMA-IR), and metabolic syndrome score (MetS score) per 1 SD increase in body composition and fitness variables. Fat mass index, % fat mass and body mass index were all strongly associated with gestational diabetes (ORs: 1.72-2.14, P ≤ 0.003), HOMA-IR (ORs: 3.01-3.80, P < 0.001), blood pressure (ORs: 1.81-2.05, P < 0.001) and MetS score (ORs: 3.29-3.71, P < 0.001). Associations with fat-free mass index were considerably weaker (ORs: 1.26-1.82, P = 0.001-0.15) and were strongly attenuated after adjustments for fat mass index (ORs: 0.88-1.54, P = 0.039-0.68). Finally, greater cardiorespiratory fitness was associated with lower risk of high HOMA-IR and MetS score (ORs: 0.57-0.63, P ≤ 0.004) although these associations were attenuated when accounting for fat mass index (ORs: 1.08-1.11, P ≥ 0.61). In conclusion, accurately measured fat mass index or % fat mass were strongly associated with gestational diabetes risk and markers of cardiovascular health although associations were not stronger than the corresponding ones for body mass index. Fat-free mass index had only weak associations with gestational diabetes and cardiovascular health which support that the focus during clinical care would be on excess fat mass and not fat-free mass.