Food analysis is a tremendously broad field that is constantly evolving. New methods have emerged to increase productivity, such as modern miniaturized and robotic analytical techniques. In this paper, a micro-solid-phase extraction system (µ-SPE) for clean-up was combined with a robotic autosampler to yield ready-to-analyze extracts. The system was evaluated for its applicability in routine laboratories. The new, automated, high-throughput µ-SPE clean-up method was applied to acetonitrile extracts and was developed for the analysis of pesticide residues in cereals by gas chromatography-Orbitrap mass spectrometry (GC-Orbitrap-MS). The µ-SPE clean-up efficiency was demonstrated in the removal of matrix-interfering components and in the recovery of pesticides. The sorbent bed mixture consisted of magnesium sulfate, primary-secondary amine, C18, and CarbonX, and effectively retained matrix components without loss of target analytes. Analysis of five types of cereals (barley, oat, rice, rye, and wheat) by GC-Orbitrap-MS showed that the method removed more than 70% of matrix components. The clean-up method was validated for 170 pesticides in rye, 159 pesticides in wheat, 142 pesticides in barley, 130 pesticides in oat, and 127 pesticides in rice. Spike recovery values were 70–120% for all pesticides and the repeatability, calculated as the relative standard deviation, was less than 20%. The limits of quantitation achieved were 0.005 mg kg−1 for almost all analytes, ensuring compliance with the maximum residue limits.