Background: Tomato is considered as “protective foods” because of its special nutritive values which are very low in fat and have zero cholesterol level, with an excellent source of lycopene, carotene, anthocyanin, antioxidants, dietary fiber, minerals, and vitamins. Objective: The objective of the study was to investigate the occurrence of pesticides and to analyze the secondary metabolite differences in selected organic and inorganic tomatoes (Variety: Sivam). Materials and Methods: The samples were analyzed for nearly 167 pesticides using gas chromatography–mass spectrometry and liquid chromatography/tandem mass spectrometry. Results: The samples were analyzed for nearly 167 pesticides in which pesticide residues were found to be absent in organic tomatoes; however, inorganic samples indicated the presence of aldoxycarb (aldicarb sulfone) and pymetrozine. The organic tomatoes contain nearly 27 phytocomponents out of which 9,12-octadecadienoic acid (Z, Z)-, methyl ester (15.68%), 9,12,15-octadecatrienoic acid, (Z, Z, Z)- (12.78%), 9,12-octadecadienoic acid (Z, Z)- (10.26%), ethyl oleate (9.48%), linoleic acid ethyl ester (8.09%), oleic acid (7.60%), pentadecanoic acid, ethyl ester (5.08%), n-hexadecanoic acid, and dl-α-tocopherol (4.90%) are major groups, whereas 24 components were noticed in inorganic samples where 9,12,15-octadecatrienoic acid, (Z, Z, Z)- (23.77%), 9,12-octadecadienoic acid (Z, Z)- (11.27%), n-propyl 9,12-octadecadienoate (10.93%), ethyl oleate (8.43%), n-hexadecanoic acid (7.69%), linoleic acid ethyl ester (7.52%), hexadecanoic acid, ethyl ester (4.06%), and dl-α-tocopherol (3.78%) were majorly found. Conclusion: Organic tomatoes selected were found to be free from pesticide residues with majority of phytocompounds at higher peaks which are found to be beneficial to fight against many diseases.