The Mediterranean Sea is at the transition between temperate and tropical air masses and as such of importance for studying climate change. The Gulf of Taranto and adjacent SW Adriatic Sea are at the heart of this region. Their sediments are excellently suited for generating high quality environmental records for the last millennia with a sub-decadal resolution. The quality of these records is dependent on a careful calibration of the transfer functions used to translate the sedimentary lipid signals to the local environment. Here, we examine and calibrate the UK′37 and TEX86 lipid-based temperature proxies in 48 surface sediments and relate these to ambient sea surface temperatures and other environmental data. The UK′37 -based temperatures in surface sediments reflect winter/spring sea surface temperatures in agreement with other studies demonstrating maximum haptophyte production during the colder season. The TEX86-based temperatures for the nearshore sites also reflect winter sea surface temperatures. However, at the most offshore sites, they correspond to summer sea surface temperatures. Additional lipid and environmental data including the distribution of the BIT index and remote-sensed chlorophyll-a suggest a shoreward increase of the impact of seasonal and spatial variability in nutrients and control of planktonic archaeal abundance by primary productivity, particle loading in surface waters and/or overprint by a cold-biased terrestrial TEX86 signal. As such the offshore TEX86 values seem to reflect a true summer signal to the effect that offshore UK′37 and TEX86 reconstruct winter and summer temperature, respectively, and hence provide information on the annual temperature amplitude.