The issue of mycotoxin contamination in food is particularly important for consumer safety. The consumption of these fungi can cause genetic mutations or lead to the formation of cancer cells. For years, foods have been studied for this problem, but for table olives, there is currently a significant lack of scientific literature. This study aimed to point out the possible application of the Enzyme-Linked Immunosorbent Assay (ELISA) method for the detection of mycotoxins in table olives, assessing the presence of aflatoxins and ochratoxin A. Different tests were carried out on commercial and inoculated olives to assess the efficacy of the method by comparison with the conventional one, based on Liquid Chromatography–Tandem Mass Spectrometry (LC–MS/MS). Initial unsatisfactory results led us to refine the extraction method via the substitution of the chemical extractant 70% methanol with dichloromethane; this procedure allowed for improving the recovery of inoculated mycotoxins. The results show the effectiveness of the ELISA test, especially in mycotoxin recovery, after the modification of the extraction method. The recoveries increased for aflatoxins from 55% to over 70% and for ochratoxin A from 40% to over 55%. When samples were analyzed with commercial kits, the results showed some false positives, especially for the first sample of ochratoxin A, but the reliability of the ELISA method test was largely verified in the rest of the samples. The validity, the reduced cost, and the speed of application of the ELISA test make this method suitable as a control program for mycotoxin detection in table olives, which can be supported by LC-MS/MS analysis in case of positive results.