Smartphone applications (SPA) now offer the ability to provide accessible in-home monitoring of relevant individual health biomarkers. Previous cross-sectional validations of similar technologies have reported acceptable accuracy with high-grade body composition assessments; this research assessed longitudinal agreement of a novel SPA across a self-managed weight loss intervention of thirty-eight participants (twenty-one males, seventeen females). Estimations of body mass (BM), body fat percentage (BF%), fat-free mass (FFM) and waist circumference (WC) from the SPA were compared with ground truth (GT) measures from a dual-energy X-ray absorptiometry scanner and expert technician measurement. Small mean differences (MD) and standard error of estimate (SEE) were observed between method deltas (ΔBM: MD = 0·12 kg, SEE = 2·82 kg; ΔBF%: MD = 0·06 %, SEE = 1·65 %; ΔFFM: MD = 0·17 kg, SEE = 1·65 kg; ΔWC: MD = 1·16 cm, SEE = 2·52 cm). Concordance correlation coefficient (CCC) assessed longitudinal agreement between the SPA and GT methods, with moderate concordance (CCC: 0·55–0·73) observed for all measures. The novel SPA may not be interchangeable with high-accuracy medical scanning methods yet offers significant benefits in cost, accessibility and user comfort, in conjunction with the ability to monitor body shape and composition estimates over time.