The excellent properties of polyether ether ketone (PEEK) have made it applicable for high-performance components in aerospace, electrical, chemical, and biomedical industries. Material extrusion (MEX) additive manufacturing (AM) of PEEK using fused filament fabrication (FFF) predominantly uses modified PEEK filament. Fused granulate fabrication (FGF) systems conventionally employ injection moulding and extrusion grades which are not specifically formulated for MEX AM. There is a limited amount of research on the use of these grades for MEX AM using PEEK. This study evaluated different viscosity PEEK grades at various extruder temperatures to optimise interlayer strength and therefore determine the best grades of PEEK for FGF. Compression shear testing (CST) was used to study this property as it represents a mostly shear loading condition i.e., without bending, compared to other conventional shear testing methods, whilst also being easier to fabricate. PEEK crystallinity is corelated to the interlayer strength and was evaluated using differential scanning calorimetry (DSC), Raman spectroscopy and X-ray diffraction (XRD). The highest interlayer strength of 17.70±0.58 MPa and the lowest crystallisation degree of 29.7±1.3% (Raman) was achieved by VESTAKEEP L4000G PEEK, printed at the highest extruder temperature (420°C). This grade had the highest viscosity or the lowest melt volume-flow rate (MVR). In contrast with lower MVR grades, the high MVR grade VESTAKEEP L2000G, achieved a higher increase in bond strength and crystallinity with higher extruder temperatures. At lower MVR, the crystallinity was found to decrease from 33% to 30% with increasing extruder temperatures, along with an increase in melting temperature. This behaviour was attributed to a change in crystalline morphology possibly caused by the long residence time and high processing temperature of FGF.