In integrated crop‐livestock‐forestry (ICLF) systems, an agroforestry model, the forestry component influences the distribution of photosynthetically active radiation (PAR) and alters grain productivity. The aim of this study was to evaluate the effects of systematic and selective thinning of eucalyptus stands on the productivity of soybean and maize grown. The randomized block‐designed experiment comprised three treatments, namely crops grown under full sunlight (CFS) and in ICLF plots subjected to systematic and selective thinning to leave single‐row (ICLFS) and triple‐row (ICLFT) tree configurations. Soybean and maize were planted in succession between the tree stands and PAR incidence/transmittance and crop productivities were evaluated in the north and south sun‐exposed faces of the plots during three cultivation cycles after thinning. In comparison with CFS, PAR transmittance in the ICLF systems decrease varied according to the time of day, period of the year, distance of the sampling position from the trees, the sun‐exposed area (north and south faces) and time after thinning. Soybean productivities in ICLFS were similar to those of CFS in the first and second crop cycles, but significantly lower (p < 0.05) in the third crop cycle. In the ICLFT system, soybean productivity was similar to that of CFS in the second crop cycle but significantly lower in the first and third crop cycles. With regard to the maize crop, productivities decreased in the order CSF > ICLFS > ICLFT in all cultivation cycles. Our results showed that PAR transmittance and soybean/maize productivities were positively influenced by thinning of eucalyptus stands, particularly in ICLFS system.