Crop–livestock integration fosters a holistic view of the agricultural system, which is nowadays particularly relevant due to the rising environmental concerns. Laying hens can contribute to improvement of soil chemical properties, but their effects in soil fertility are not fully known. This study aimed to evaluate the effects of grazing laying hens on soil fertility. To meet this goal, we assessed the effects of indigenous laying hens in 22 soil parameters, including chemical, physical, and microbiological parameters, in two farms from the central region of Portugal: an organic horticultural field (A) and a conventional orchard (B). At farm A, the animals grazed during the dry period for 84 continuous days, at a density of 4 m2 per hen. At farm B, the animals grazed during the wet period, at a density of 3.50 m2 per hen, in two periods (34 + 33 days), with a 50 day break period in between grazing. The hens contributed to an increase in the extractable macronutrients phosphorus (P2O5) and potassium (K2O), mineral nitrogen (NH4+-N and NO3−-N), and exchangeable bases calcium (Ca2+) and magnesium (Mg2+) in both farms, making these central parameters to consider in their grazing management. At farm A, where soil disturbance is higher, the grazing did not affect soil moisture retention but positively affected soil dry bulk density and contributed to an increase in total aerobic bacteria and nitrogen-fixing bacteria abundances. At farm B, where the hens’ presence led to the understory eradication, soil moisture retention, total aerobic bacteria, nitrogen-fixing bacteria, and fungi abundances were negatively affected, while soil dry bulk density was unaffected. These results show that hens can significantly contribute to improve soil fertility, but more research is needed regarding their grazing management.