Synthetic cannabinoids (SCs) remain one of the largest groups of new psychoactive substances. Recently, new synthetic cannabinoids 5F-MDMB-PICA and 4F-MDMB-BINACA are increasing in popularity. A 33-year-old man lost consciousness after smoking an unknown substance. A glass pipe and two lumps of substance that turned out to contain 5F-MDMB-PICA and 4F-MDMB-BINACA were found at the scene. Blood, urine and cerebrospinal fluid were collected during the examination of the body. The synthetic cannabinoids were isolated from autopsy materials by precipitation with acetonitrile and extraction with ethyl acetate. The screening and quantitative analyses were performed by liquid chromatography with tandem mass spectrometry (LC–MS/MS). The liquid chromatography-quadrupole/time of flight mass spectrometry (LC–Q/TOF) technique was used for metabolite identification. 5F-MDMB-PICA was detected and quantified in all analysed materials, whereas 4F-MDMB-BINACA was found only in cerebrospinal fluid. The determined concentrations of 5F-MDMB-PICA were 0.9 (blood), 0.1 (urine) and 3.2 ng/mL (cerebrospinal fluid). The concentration of 4F-MDMB-BINACA in cerebrospinal fluid was 0.1 ng/mL. The main metabolites of both compounds (hydrolysis and oxidative defluorination) were found in all analysed body fluids. Cerebrospinal fluid may be important alternative material in autopsy cases. Rapid elimination of 5F-MDMB-PICA and 4F-MDMB-BINACA compounds also means that the metabolite analysis can be crucial for the investigation. Laboratories must be made aware of their presence and incorporate these SCs and their metabolites into workflows for detection and confirmation. Ester hydrolysis and oxidative defluorination products can be found in blood, urine and cerebrospinal fluid making them useful biomarkers of intake.