The relevance of the linker tethering site in haptens was investigated for antibody generation and immunoassay development. Three derivatives of the strobilurin fungicide picoxystrobin were synthesized with the same functionalized spacer arm located at three different positions. Protein conjugates of those haptens were employed as immunogens and novel polyclonal antibodies were produced and characterized. All haptens afforded highly specific antibodies, but different affinities to the free analyte were observed among the obtained antisera. Then, competitive enzyme-linked immunosorbent assays were studied in several formats, and site heterology was confirmed as an effective strategy for detectability improvement. An indirect heterologous immunoassay was eventually selected and optimized, showing a limit of detection for picoxystrobin of 0.02 µg/L and a working range between 0.03 and 1.30 µg/L. Finally, the developed extraction and analytical procedures revealed a practical limit of quantification of 5 µg/kg for this fungicide in soybean sprouts, well below the maximum residue limits in the EU.