Energy deficit (via calorie restriction and/or exercise) induces weight loss and improves metabolic outcomes. Importantly, calorie restriction elicits benefits that are distinct from exercise training, most noticeably in improving maximal lifespan and some markers of primary aging. We aimed to distinguish the effect of calorie restriction from energy deficit per se on adipose-transcriptomic response in humans. Abdominal subcutaneous fat was collected, at baseline and 6-months, from 24 overweight participants (12M/12F; BMI 27.6±1.6 kg/m2; age 38±6 y) randomized in the following groups (N=8/group): weight maintenance (control), 25% energy deficit by calorie restriction alone (CR) and 25% energy deficit by calorie restriction and structured exercise (CREX) with no difference in BMI and age across groups. Illumina cDNA microarrays were used for transcript profiling. Gene expression was compared between 6-months and baseline within each group with cut-offs at nominal P < 0.01 and absolute log of the 6-months-to-baseline ratio ≥ 0.58. Microarray data were subjected to gene-set enrichment analysis (KEGG) with significance cut-off at a false discovery rate < 5%. CR and CREX elicited similar clinical response after 6 months of intervention and comparable effects on reducing gene transcription specific to oxidative phosphorylation and proteasome function. CR vastly outweighed CREX in the total number of differentially regulated genes (88 vs 39) and pathways (28 vs 6). CR-specific down-regulation of the inflammation-regulated pathways was observed. At the gene level, 27 of the CR-regulated genes were transcription/translation regulators (e.g. RNA splicing, histone methylation or transcription/translation initiation), whereas CREX regulated only 1 gene in this category. Our data showed that CR had a more diverse impact on the transcriptome as compared to energy deficit per se. The effect of CR on the transcription/translation regulators may be one of the key molecular mechanisms by which CR confers benefits at a systemic level and on primary aging.