Lack of soft wheat variety and classification of wheats according to end product, baking industry faces continuous problems with the stability and quality of products. The current research work was undertaken to characterize different (six) Pakistani wheat varieties for physicochemical, rheological, nutritional characteristics and to check multivariate association among these characteristics with special reference to cookie quality prepared from wheats of varying extraction rates (study-I). In study-II, different levels of chemical treatments (sodium stearoyl 2-lactylate (SSL), L-cysteine and Lecithin) and shortenings (fat, oil, and margarine) were applied on mixed wheat flour to choose best level on the basis of sensorial and physical characteristics of cookies. Furthermore, selected levels of chemical treatments, shortening and physical treatments (heat) were compared regarding sensory, physico-chemical and nutritional attributes of cookies (study-III). Significant variation among wheat varieties were observed with respect to particle size index (PSI), thousand kernel weight (TKW), test weight (TW), pearling value, water solvent retention capacity (WSRC), sodium carbonate solvent retention capacity (SCSRC) and dough rheological parameters. Fatty acids like, Stearic, Elaidic, Caprylic acids were observed abundantly in wheat flours, and comparatively better fatty acid profile was observed in “Punjab 2011” and “Galaxy 2013”. Cookies prepared from flours of varying extraction rate imparted significant variation on color and overall acceptability of cookies while interaction of wheat variety and extraction rate imparted significant (p<0.05) variation on taste and texture of cookies. In most of the sensory parameters, it was observed that cookies prepared from high extraction rate i.e. 72-74% (stream split flour) gained high score and among wheat varieties, cookies prepared from flour of “Millat 2011” attained better score than cookies prepared from flour of other wheats. Spread factor (SF) of cookies was correlated with PSI (r = -0.63), pelshenke value (r = -0.62), water absorption (WA) (r = -0.60) and mixographic peak height (MPH) (r = 0.85).Principal Component Analysis (PCA) showed that PC1 accounted for 30.68% of variation for MPH, SF, peak viscosity, breakdown viscosity and damaged starch being the major factors. While, PC2 accounted for 21.29% variation with flour rheological properties like dough development time, dough stability, pasting temperature, trough viscosity, falling number and TW were the major factors. Based on sensory and physical characteristics (diameter, thickness, spread factor and textural hardness), it was concluded that “T1” (SSL @ 0.5%), “T4” (L-cysteine @ 0.5%), “T9” (oil + margarine) and “T11” (lecithin @ 1%) provided better quality cookies when applied on mixed wheat flour during study-II. In study–III, significant deviation in physical parameters like diameter (3.96-4.66cm), thickness (0.99-1.21cm), spread factor (37.32-46.03), color like L* (58.99-70.01), a* (0.80-2.61), b* (15.36-22.37) and hardness (2.09-2.89) of cookies was observed due to selected treatments. Among these, cookies prepared from Lecithin (@ 1%) and SSL (@ 0.5%) got high score in sensory evaluation, in textural hardness cookies prepared with SSL showed better results and regarding spread factor of cookies best results were observed in SSL (@ 0.5%) and in lecithin (@ 1%). Among fatty acids of cookies, abundantly found fatty acids were palmitoleic acid, stearic acid, myristoleic acid and oleic acid. Highest amount of palmitoleic acid (9.84%) and stearic acid (8.81%) was observed in “T4” (Lecithin @1%) while least amount was observed in “T3” (oil + margarine) and “T1” (SSL @ 0.5%) respectively. Therefore, current study suggested that SSL @ 0.5% and lecithin @ 1% can be incorporated in cookie recipe to minimize variation (occurred due to mixed wheat flour) in quality attributes of cookies.