Boron (B) and zinc (Zn) deficiencies are widespread in alkaline, calcareous and low organic-matter soils of Pakistan. In the present study, the Cotton crop responded positively to application of B and Zn fertilizers. Plant growth, productivity and nutritional value of cottonseeds were improved, very cost-effectively, by optimizing B nutrition. Fertilizer B requirement was 1.0 kg B ha-1 and HCl extractable soil B critical range appears to be 0.5-0.6 mg kg-1 soil. . Similarly, use of Zn fertilizer in cotton promoted seed cotton yield, boll bearing, boll weight, and seed index. Zn application at rate of 7.5 kg ha−1 was most cost-effective. Certain plant physiological parameters, such as membrane integrity and chlorophyll content, were improved with better Zn nutrition of plants. Moreover, both B and Zn fertilizers showed residual effects in cotton - wheat system.