An experiment was conducted at Mahatma Phule Krishi Vidyapeeth (MPKV), Rahuri a representative place for the vertisols of Deccan plateau of India to study the effect of organic and inorganic fertilizers on crop yield and soil physical, chemical and biological properties in the cotton-chickpea cropping sequence. There were seven treatments applied to hybrid cotton and each plot of summer cotton was equally divided into four parts to chickpea. Application of Recommended Dose of Fertilizer (RDF) according to Soil Test Crop Response (STCR) equation recorded significantly higher seed cotton yield and cotton equivalent yield, however it was at par with 10 t Farm Yard Manure (FYM) ha-1 + RDF. Chickpea registered significantly higher seed yield in 10 t FYM ha-1 + RDF and it was at par with 100% RDN through vermicompost. 100% RDF registered significantly superior seed chickpea seed yield and cotton equivalent yield. The soil physical, chemical and biological properties determined at the end of two crop cycles were improved due to the application of manures in sole or in combination with chemical fertilizers.