Animal studies have demonstrated that energy restricted diets and exercise affect the gut microbiome and are positively linked to physical health, however, less is known about the impacts of various patterns of dietary restriction combined with exercise on the gut microbiota and associated health outcomes. This study aimed to determine if an energy-restricted diet combined with resistance training altered the gut microbiome, and whether any changes were associated with differences in body composition, dietary intake or biomarkers of cardio-metabolic health. Twenty-six healthy males and females, aged 19-36 years with a BMI of 22-35, were enrolled in 2-arm parallel, randomised-controlled trail and followed either a 5:2 intermittent fasting (IFT, N=13) or continuous energy restriction (CERT, N=13) diet combined with supervised resistance training for 12 weeks. 16S rRNA based metagenomic analysis revealed that the effect of both interventions on gut microbiome diversity was not greater than interindividual differences. The CERT group experienced greater reductions in Bacteroidetes (CERT, -2.8 fold, p<0.02; IFT, -1.7 p=n.s) while there were minor increases in Firmicutes (CER, 1.06 fold; IF, 1.007 fold). Both treatments resulted in decreased body weight and increased lean body mass. Shifts in the abundance of, Faecalibacterium prausnitzii, a major butyrate producer was positively associated with changes in lean body mass (IFrs=.58, p=0.05, CERrs=.69, p=0.01). Moreover, in the CERT group, changes in energy and fat intake were negatively associated with Coprococcus genus (rs=-0.7, p=0.009, rs=-0.59, p= 0.03). Interestingly, participants who experienced greater reductions in the Coprococcus genus (rs=0.67, p=0.02) also had greater reductions in body fat when controlling for energy and fat intake. Overall, the findings indicate that diets restricted in total energy intake have little effect on gut microbiota, but changes that did occur were associated with measures of physical health, providing further support to the relathinship between gut microbiota, energy consumption and physical health.