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Multiparametric toxicology research is mainly based on immunochromatography (IC) and chromatography methods. A new automated method using an immunoenzymatic (IE) assay based on biochip array technology combines a short turnaround time and analytical performances similar to chromatography in terms of positivity cut-off. The aim of our study was to compare IE with IC and chromatography methods using urine samples from clinical cases. Seventy-two samples were analyzed using IC (amphetamines, opiates, benzodiazepines, THC, methadone, cocaine), IE, and chromatography (previous classes plus opioids and cathinone). The IC results were read by at least 7 operators to assess reading subjectivity. The IE, IC, and chromatography results were compared with each other. Chromatographic quantification was analyzed to understand discrepancies. Significant discrepancies (29–64%) were observed between IC and IE for most of the drug families investigated except for benzodiazepines, methadone, and opiates. These discrepancies were not identified between IE and chromatography, except for some substances (28%–67% discrepancies for buprenorphine, tramadol, and oxycodone, 100% for cathinone). In contrast to IC, the performance of IE neared those of chromatography, except for some substances for which cross-reactions need to be investigated. Reading discrepancies were frequent with IC (33% of samples) and made robust result output challenging. In conclusion, Multistat® is an interesting method for first-line toxicological screening for laboratories that don’t use the chromatography method.