Intensive agriculture in South Asia has resulted in soil degradation and loss of crop production potential. Soil health is a key factor in crop production and the new emphasis on sustainable agriculture has generated interest in the optimization of all aspects of soil functioning - physical, chemical and biological. The objective of this study was to use a set of soil health indicators to measure the effects of farm manure (FM) application and cropping pattern on Pakistan soils. For this study five cropping systems, i.e. cotton-wheat (CW), maize-wheat (MW), rice-wheat (RW), sugarcane-wheat (SW) and vegetable-vegetable (V-V), both, manured and non-manured were selected from each cropping zones of Pakistan. Samples collected were analyzed for soil health indicators including soil bulk density, available water capacity (AWC), aggregate stability (WSA), macro porosity, organic matter (OM), soil active carbon (ActC), potentially mineralizable nitrogen (PMN), P, K, Zn, Ca, S, CEC and pH. Manured plots had significantly higher levels of OM (28%), ActC (43%), PMN (92%), AWC (24%), and macro porosity (19%) and significantly lower bulk density (5%) than non-manured plots. Among cropping systems highest values were found in SW, MW and SW compared to RW, with higher values in the former systems for WSA (243%), AWC (16%) and macro-porosity (39%). This clearly gave indication of the deteriorative effect of puddling in rice cultivation. Higher values were observed in MW, RW, CW with higher OM (36%), active carbon (ActC, 33.6%) and PMN (731%) compared to CW and VV. Only S and Mg were significantly higher in manured plots while pH, CEC, NO3-N, P, K, Zn and Ca were statistically not different in manured fields. Results of this study conclude that long-term manure applications improve soil quality, while puddling, especially in rice cultivation, exhibits maximum damage to soil physical quality indicators. (C) 2014 Friends Science Publishers