Pakistan is predominantly an arid country but it has one of the best and extensive irrigation systems in the world. Wheat (Triticum aestivum L.) and rice (Oryza sativa L.) are the major grain crops in the country and wheat-rice cropping pattern is followed on substantial area of the country. Soil health directly controls the growth and development of crops and so for wheat and rice. The key of sustainable agricultural production is the optimum use of on-farm resources to feed ever increasing population without harming the available resources. For seed bed preparation the use of different tillage methods is most likely and is in practice for many years. Depending upon soil type and agro- ecological conditions of a particular area, appropriate tillage methods should be selected. Soil quality is affected by tillage and farm manure application, similarly, crop growth and yield is also controlled to various degrees. In order to assess the effect of farm manure, compost and inorganic fertilizer on the growth and yield of wheat and rice crops, pot studies were conducted. The promising level of farm manures from these studies and from previous literature were chosen for field studies. The use of different tillage systems is common practice of the regional farmers. The effects of tillage and farm manure on crop growth and yield, soil physical properties and C-sequestration under wheat-rice cropping rotation were investigated at Faisalabad. Three tillage methods (minimum, conventional and deep tillage) and three farm manure at 0 (control), 15 and 30 Mg ha–1 was used to evaluate the effect on soil physical properties and growth. The wheat and rice crops were sown in pots and field up to maturity. Different agronomic, yield parameters and chemical composition were recorded at the harvest of each crop. Soil samples (0-100 cm) were collected before and after every crop from each treatment plot and were analyzed for NPK concentrations. Soil bulk density and hydraulic conductivity was improved by the use of farm manure. Data were analyzed statistically following standard statistical procedures analysis of variance and multivariate analysis of variance and bi plots were constructed. The root length density (RLD) of wheat in upper 10 cm soil layer was 16% more in case of minimum tillage (MT) with farm manure at 30 Mg ha–1 (FM30). The total RLD of rice the same soil layer was increased by 12% and 17% in case of deep tillage with FM at 15 Mg ha–1. The rice yield was increased by 24% under minimum tillage with FM30 during first year and 21% at 15 Mg ha–1 FM under same tillage. The increase in wheat yield was 11% under MT with farm manure at 15 Mg ha–1 (FM15) during second year. The conventional tillage (CT) with FM30 increased the carbon sequestration among all the tillage systems. The information will be used to further evaluate the amount, direction and change in carbon turnover in all the cropping systems of the country to alleviate the resource poor farmers of the country and in the long run to assess the value of different indicators in relation to soil quality and crop productivity. The treatment combinations CT × FM0 (first year) and CT × FM15 (second year) were more economical incase of wheat. CT × FM15 also proved its worth incase of rice for both years.