In cotton–wheat cropping system of Pakistan, wheat (Triticum aestivum L.) is harvested in late April; however, the optimum sowing time of Bt cotton is mid-March. This indicates a time difference of 4–6 weeks between the harvest of wheat and cotton sowing. It is hypothesized that this overlapping period may be managed by transplanting cotton seedlings (30–45 days old) in late April, after the harvest of wheat due to better performance of already established seedlings. To this end, this study was conducted to evaluate the allometric traits and fiber quality of transplanted Bt cotton after harvesting wheat in the cotton–wheat cropping system. The Bt cotton–wheat cropping systems were flat sown wheat (FSW)–conventionally tilled cotton, FSW–zero tilled cotton, ridge sown wheat–ridge transplanted cotton using 30- and 45-days-old seedlings, and bed sown wheat (BSW)–bed transplanted cotton (BTC) also using 30- and 45-days-old seedlings. The study was conducted at Vehari and Multan in Punjab, Pakistan. Bt cotton in BSW–BTC with 45-days-old seedlings showed better performance for allometric (leaf area index; (LAI), net assimilation rate; (NAR), and crop growth rate; (CGR)), seed cotton yield, and fiber traits (fiber uniformity, fiber length, fiber strength, and fiber fineness) in comparison to other treatments. Most of the fiber quality traits were positively correlated with allometric traits and biological yield (dry matter yield at maturity) at both locations, except correlations of CGR and LAI with fiber fineness and fiber length and NAR with fiber length. As plant growth and fiber quality of transplanted cotton was significantly higher than conventionally grown cotton, our data indicate transplanting is an interesting management practice for improving productivity in wheat–cotton cropping systems.