A new method for the analysis of three ecological insecticides, namely azadyrachtin, spinosad (sum of spinosyn A and spinosyn D) and rotenone, in produce and soil samples is presented. Investigated compounds are one of the most significant insecticides authorized for organic farming crop protection in many countries. Extraction of the pesticides from plant and soil matrices was performed by using a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. The method entailed a single extraction of the investigated compounds with acidified acetonitrile followed by a dispersive solid-phase extraction cleanup step prior to the final determination by reverse-phase ultra-performance liquid chromatography/tandem quadrupole mass spectrometry (UPLC-MS/MS). Validation studies were carried out on cabbage, tomato and soil samples. Recoveries of the spiked samples were in the range between 67% and 108%, depending on the matrix and the spiking level. Relative standard deviations for all matrix–compound combinations did not exceed 12%. The limits of quantification were ≤0.01 mg kg−1 in all cases, except for azadirachtin. The developed method was applied to the analysis of real samples originating from organic farming production.