Analytical method development for the control of pesticide residues occurring in significant dietary foodstuffs is of utmost importance considering their potential impact on consumer health and food market sustainability. Depending on the purpose, either instrumental analysis, mainly chromatographic methods, or screening assays, mostly using biorecognition affinity, are commonly used, featuring different advantages and drawbacks. To practically compare these two different types of analytical strategies, we applied them for the detection of (i) 97 organophosphate (OP) and carbamate (CM) pesticide residues in wheat flour and (ii) carbofuran (a carbamate insecticide) in wheat, rye and maize flour samples. Regarding high-end analysis, an ultra-high-performance liquid chromatography coupled with triple quadrupole mass spectrometry (UHPLC-QqQ-MS) method was developed and validated achieving low limits of quantification (LOQs, from 0.002 to 0.040 mg kg-1) and a short chromatographic run (12 min). In terms of bioanalytical methods, a fast (17 min) and cost-efficient (∼0.01€ per sample) acetylcholinesterase (AChE) microplate assay for carbofuran screening was utilized. Importantly, carbofuran was the strongest of the 11 OP and CM tested pesticides achieving a half maximal inhibitory concentration (IC50) of 0.021 μM whilst the assay detectability was at the parts per billion level in all three cereal matrices. Based on the attained results, a critical discussion is presented providing the analytical merits and bottlenecks for each case and a wider outlook related to the application of analytical methods in the food safety control analytical scheme.