Sorghum-cowpea intercropping is the most common cropping system in the Sub-Saharan region of Burkina Faso where soil fertility is low. One of its specificity is the sowing of the both species in the same zaï holes. This study analyzes the variability of nodulation and growth of cowpea, and their relations according to organic fertilization, farmer’s field, and years. Two treatments with and without organic substrates, namely ZF and ZS, respectively, were compared in 12 field trials established during years 2012, 2013 and 16 field tests during 2014, in 3 villages in the north of Burkina. The results showed that the nodulation and shoot growth of cowpea, varied among sites and years, and were higher under ZF than ZS, whatever the year. The nodulation variability depended upon organic substrate P and N in 2014 under ZF, and upon soil P bio-availability in 2012, 2013 and 2014 under ZS. Under ZS, the mean efficiency of individual nodule to support shoot dry weight was 0.6 ± 0.2 and 4.0 ± 1.6 g shoot dry weight per nodule in 2014 and 2012, respectively. In 2013, there was no significant correlation between growth and nodulation, which could be explained by low average rainfall. In 2014 under ZS, the high efficiency in use of the rhizobial symbiosis of cowpea plant was 128.5 ± 35.4 g shoot dry weight per g nodule dry weight and the N derived from nodule N2 fixation could be estimated as 510.9 ± 127.1 mg N per g nodule dry weight. It is concluded that the measurements of nodulation and growth of cowpea at flowering stage may contribute to optimize the organic fertilization of cowpea in zaï intercropping with sorghum and the subsequent improvement of crop yields in Northern-Burkina Faso.