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Background: This study evaluates whether the initial amount of dietary protein intake could influence the combined effect of high-intensity interval training (HIIT) and citrulline (CIT), or HIIT alone, on body composition, muscle strength, and functional capacities in obese older adults. Methods: Seventy-three sedentary obese older men and women who completed a 12-week elliptical HIIT program with double-blinded randomized supplementation of CIT or placebo (PLA) were divided into four groups according to their initial protein intake (CIT&#8722;PROT+: <i>n</i> = 21; CIT&#8722;PROT&#8722;: <i>n</i> = 19; PLA&#8722;PROT+: <i>n</i> = 19; PLA&#8722;PROT&#8722;: <i>n</i> = 14). Body composition (fat and fat-free masses), handgrip (HSr) strength, knee extensor (KESr) strength, muscle power, and functional capacities were measured pre-intervention and post-intervention. Results: Following the intervention, the four groups improved significantly regarding all the parameters measured. For the same initial amount of protein intake, the CIT&#8722;PROT&#8722; group decreased more gynoid fat mass (<i>p</i> = 0.04) than the PLA&#8722;PROT&#8722; group. The CIT&#8722;PROT+ group increased more KESr (<i>p</i> = 0.04) than the PLA&#8722;PROT+ group. In addition, the CIT&#8722;PROT&#8722; group decreased more gynoid FM (<i>p</i> = 0.02) and improved more leg FFM (<i>p</i> = 0.02) and HSr (<i>p</i> = 0.02) than the CIT&#8722;PROT+ group. Conclusion: HIIT combined with CIT induced greater positive changes than in the PLA groups. The combination seems more beneficial in participants consuming less than 1 g/kg/d of protein, since greater improvements on body composition and muscle strength were observed.