With aim of assessing inter-laboratory variations, phytochemical and antioxidant analysis of seventeen wheat lines were carried out in three well-equipped Indian laboratories viz- National Agri-Food Biotechnology Institute (NABI), Punjab, Central Institute of Post-Harvest Engineering & Technology (CIPHET), Punjab, and National Institute of Nutrition (NIN), Telangana. Protocols were rigorously discussed among laboratories, re-formulated, and uniformly executed for estimating anthocyanins, phenolics, flavonoid content and antioxidant activity measured by colorimetric assays (DPPH, ABTS, FRAP & MC). Compiled data complement each other, with minor inter-laboratory variations. Colored wheat lines show higher antioxidant activity and phytochemical profile than white wheat lines across the laboratories. Within colored wheat lines, black wheat lines have the best nutraceutical profile across the laboratories, with an observed order of black > blue > purple > white. Within black wheat varieties, one of the studied lines, Bk2, consistently outperformed across the laboratories and had highest antioxidant activity, mean anthocyanin content (150.19 mg/kg), phenolic content (277.67 mg/kg), flavonoid content (17.76 mg/kg). The factors that may contribute to the evaluation process include differences in the human resources involved, type and company of solvent, instrument model, and weather and humidity conditions during the measurement. This study validates the higher phytochemicals and antioxidant property of colored wheat through a multi-laboratory analysis.