This study described the whole blood fatty acid profile and Omega-3 Index (O3I) of Australian Army recruits at the commencement and completion of basic military training (BMT). Eighty males (17–34 y, 77.4 6 13.0 kg, 43.5 6 4.3 mL/kg/min) and 37 females (17–45 y, 64.3 6 8.8 kg, 39.3 6 2.7 mL/kg/min) volunteered to participate (N = 117). Whole blood samples of each recruit were collected using a finger prick in weeks 1 and 11 (n = 82) and analysed via gas chromatography for the relative proportions of each fatty acid (mean [95% confidence interval]). The macronutrient characteristics of the diet offerings was also determined. At commencement there was a low omega-3 status (sum of omega-3; 4.95% [4.82–5.07]) and O3I (5.03% [4.90–5.16]) and no recruit recorded an O3I >8% (desirable). The omega-6/omega-3 (7.04 [6.85–7.23]) and arachidonic acid/eicosapentaenoic acid (AA/EPA) (18.70 [17.86–19.53]) ratios for the cohort were also undesirable. The BMT mess menu provided a maximum of 190 mg/day of EPA and 260 mg/day of docosahexaenoic acid (DHA). The O3I of the recruits was lower by week 11 (4.62% [4.51–4.78], p < 0.05), the omega-6/omega-3 increased (7.27 [7.07–7.47], p < 0.05) and the AA/EPA remained elevated (17.85 [16.89–18.81]). In conclusion, Australian Army recruits’ omega-3 status remained undesirable during BMT and deserves nutritional attention. Novelty: Australian Army recruits’ Omega-3 Index, at the commencement of BMT, was reflective of the Western-style diet. The BMT diet offered minimum opportunity for daily EPA and DHA consumption. Every recruit experienced a further reduction of their Omega-3 Index during BMT.