Lately, there is maximum concern in most states, all over the world, regarding the levels of pesticide residues in food products, considering their chemical properties with direct implications on human health. Many studies have shown that the adverse effects of cumulative exposure to multiple pesticide residues are far more severe than any single exposure. Statistically, the number of food alerts generated by the presence of pesticide residues in fruits on the market, between 2017 and 2021, as well as the situation related to the number of imports and intra-EU trade that took place during the same period was highlighted. This study aims to analyze pesticide residue levels in citrus fruits (i.e., lemons, grapefruit, and orange) imported from non-EU and EU countries, comparative with maximum residue limits (MRLs) provided by Regulation 2005/396/EC, to assess if intake levels pose a long-term risk to human health. The citrus samples collected from ten markets (retail and storage areas) in Romania, were prepared according to the procedure provided by EN 15662:2008 standard. The concentration of pesticide residues from citrus samples was determined by Gas Chromatography-Tandem Mass Spectrometry (GC-MS/MS). The results obtained by GC-MS/MS showed that from 52 citrus samples, 41 samples contained pesticide residues with values between 0.005 and 2.700 mg/kg, and several samples contained forbidden active substances (e.g., spirodiclofen and o-phenylphenol). The pesticide detection rate of the samples was 78.84%. The most frequently detected pesticides according to obtained results were imazalil, thiabendazole, pyrimethanil, pyraclostrobin, fludioxonil, as well as spirodiclofen and o-phenylphenol. The samples with the most detected active substances are from imports outside of the European Union. In addition, in several samples, simultaneously occurred four or even five mixed pesticide residues, hazardous to human health. This study shows that the presence of pesticide residues is constant in citrus fruits due to phytosanitary treatments carried out on crops in the development phase as well as on fruits in the storage phase treatments (e.g. insecticides, fungicides, etc.).