From a fundamental and application point of view it is of importance to understand how charge carrier generation and transport in a conjugated polymer (CP):fullerene blend are affected by the blend morphology. In this work light-induced electron spin resonance (LESR) spectra and transient ESR response signals are recorded on non-annealed and annealed blend layers consisting of alkyl substituted thieno[3,2-b]thiophene copolymers (pATBT) and the soluble fullerene derivative [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) at temperatures ranging from 10 to 180 K. Annealing of the blend sample leads to a reduction of the steady state concentration of light-induced PCBM anions within the blend at low temperatures (T = 10 K) and continuous illumination. This is explained on the basis of the reducing interfacial area of the blend composite on annealing, and the high activation energy for electron diffusion in PCBM blends leading to trapped electrons near the interface with the CP. As a consequence, these trapped electrons block consecutive electron transfer from an exciton on a CP to the PCBM domain, resulting in a relatively low concentration charge carriers in the annealed blend. Analysis of the transient ESR data allows us to conclude that in annealed samples diamagnetic bi-polaronic states on the CPs are generated at low temperature. The formation of these states is related to the generation and interaction of multiple positive polarons in the large crystalline polymer domains present in the annealed sample.