Abstract Hair has been used for decades in toxicology as a biological matrix for long-term detection of substances. Nails are another keratinized matrix that is being studied as an alternative when hair cannot be obtained. Although cannabis is the most prevalent illicit drug in the world, cannabinoid distribution in nails compared with hair has been scarcely studied. In this work, we described two methods for the determination of cannabidiol (CBD), cannabinol (CBN) and Δ9-tetrahydrocannabinol (THC), and main metabolites of THC [11-nor-9-carboxy-THC (THCCOOH), 11-hydroxy-THC (OHTHC) and 8-β-11-dihydroxyTHC (diOHTHC)] in nail and hair samples. After an alkaline hydrolysis, samples were submitted to solid-phase extraction and analyzed by liquid chromatography with tandem mass spectrometry (LC–MS-MS). The methods were fully validated, with good linearity (r2 > 0.99) in the range of 20 to 100 to 20,000 pg/mg. No endogenous or exogenous interferences were found. Accuracy was from 99.5% to 109.8%, and imprecision was <6.9%. Ion suppression (up to −74.4%) was observed for all the analytes, except for diOHTHC at low concentrations in hair (46.1%). Extraction efficiency ranged from 21.5% to 84.5%. The methods were applied to matched nail and hair specimens from 23 cannabis users to study the incorporation and distribution of the cannabinoids into these matrices. Only CBD, CBN and THC were detected in the samples, with much higher concentrations in fingernails than in toenails and hair. Correlations between analyte concentrations in the different matrices and with reported drug consumption were studied. A preliminary cut-off for THC in toenails was calculated using the cut-off proposed by the Society of Hair Testing in hair for the identification of chronic cannabis use.