Children generally have higher Flame Retardant (FR) concentrations in serum compared to other age groups. Toddler behavior enhances direct contact with house dust since their frequent presence proximate to the floor, and their mouthing behavior. This study aimed to thoroughly investigate FR levels in body wipes of toddlers 8–18 months old) and in indoor dust using a noninvasive sampling technique. In this cross-sectional study, body wipes from hands, mouth and back, and indoor household dust samples were collected in twenty-one families and analyzed for one brominated- and seven organophosphorus FRs (polybrominated diphenyl ether 209 (BDE209), tris(2-chloroisopropyl) phosphate (TCIPP), tris(chloroethyl) phosphate (TCEP), tris(1,3-dichloroisopropyl) phosphate (TDCIPP), tris(phenyl) phosphate (TPHP), tris(methylphenyl) phosphate (TMPP), resorcinol bis(diphenyl phosphate) and bisphenol A bis(diphenyl phosphate)). Accelerated solvent extraction was used for extraction and the extract was measured with liquid chromatography combined with mass spectrometry. Non-parametric correlation analyses were performed to assess associations. All FRs were detected in body- and indoor dust samples (median range: 1.0 ng/hand wipe (BDE209) to 65 ng/hand wipe (TCIPP)) and were mostly correlated with each other. We estimated that approximately 260 mg dust (range 50–880 mg) accumulated on toddler's hands per day. Hand-to-mouth frequency was negatively associated with FR levels in wipes (τ = −0.38, p = 0.04). With increasing age FR concentrations (BDE209, TCEP, TDCIPP, TPHP and TMPP) on hands decreased significantly (p = 0.01–0.03). Girls had significantly less FRs (TCEP, TCIPP, TPHP and TMPP) on the hands (p = 0.01–0.03) than boys. This is to the best of the authors’ knowledge the first study in Europe that measured brominated- as well as organophosphorus FRs in several types of body wipes from toddlers and that estimated the amount of house dust that accumulates on toddler's hands.