Cotton crop is highly susceptible to attack by sucking pests. Being an important oilseed and feed crop, it is essential to monitor the pesticides and ensure health protection at consumer level. Therefore, a method was validated to estimate fipronil and flonicamid in various cotton samples and risk assessment was performed. Contamination of oil in the extracts from the various oil seeds and cake samples is a major problem as this oil contaminates the column and interferes with the detection of pesticides. The present manuscript for the first time describes successful analysis of the pesticides from various cotton samples including cotton oil, seed, and cake. Quick, easy, cheap, effective, rugged, and safe (QuEChERS)-based methods were validated for estimation of fipronil and flonicamid in cotton samples and in soil by LC-MS/MS. Recoveries were within the acceptable range of 70–120% with relative standard deviation ≤ 20% and HorRat values < 0.3–1.3. R² was > 0.99. Matrix effects of 150 and 13.5% were observed for fipronil and flonicamid, respectively, in cotton leaves. Limits of quantitation (LOQs) were in the range of 0.0004 to 0.004 mg kg⁻¹ for fipronil and flonicamid. Cotton samples collected from a field study at different locations were analyzed. Half-life ranged from 2.2 to 5.8 for fipronil and 4.6 to 7.0 days for flonicamid. A pre-harvest interval of 33 days is suggested. The risk assessment studies at maximum residue level values showed HQ < 1 at pre-harvest interval (PHI). The methods being short and easy can be extended to estimate more types of pesticides in different oilseeds. Following a PHI of 33 days, fipronil and flonicamid can be used on cotton at standard dose. As the levels of fipronil and flonicamid were below determination limit in all the soils, the environmental risk is negligible.