We present an analytical method to detect and quantify residues of currently used pesticides (CUPs), which include 31 active ingredients (ai) and seven transformation products (TPs) in tropical and agricultural soils of Cuba. Ten isotopically labeled analogous compounds served as internal standards (IL-IS). The novelty of this research is the inclusion of different tropical soils type scarcely studied for CUPs and TPs, based on the QuEChERS (quick, easy, cheap, effective, rugged and safe) method, followed by chromatography tandem mass spectrometry. All figures of merit proved to be satisfactory according to SANTE guidelines 2020 and 2021. Matrix effects (ME) calculated by the external standard method were significant (|ME| > 20% for almost all compounds; grand mean ± standard deviation (STD) 104 ± 108%) in all soils. The internal standard method compensated ME to non-significant levels (8 ± 50%), even for analytes with a non-structure identical IL-IS (STD, 13 ± 57%). Repeatability (relative standard deviation, RSDr) and reproducibility (RSDR) for skeletic regosol (SR) were 7.5 ± 2.8% and 11.7 ± 4.7%, respectively. Absolute (quantified for 11 analytes with structure identical IL-IS) and relative recovery from SR was 92 ± 13% (mean ± STD) and 90 ± 12%, respectively. Limits of quantification for SR ranged from 0.1 to 10 ng/g, except metalaxyl and oxyfluorfen (25 ng/g each). Linearity of matrix-matched (MM) calibration curves (5 to 100 ng/g) had an R2 of ≥ 0.99 for all soils and almost all analytes. The method was successfully applied to 30 real soil samples.