The formation of separate phases in crystalline materials is promoted by doping with elements with different valences and ionic radii. Control of the formation of separate phases in multiferroics is extremely important for their magnetic, ferroelectric and elastic properties, which are relevant for multifunctional applications. The ordering of dopants and incipient phase separation were studied in lead titanate-based multiferroics with the formula (Pb0.88Nd0.08)(Ti0.98-xFexMn0.02)O3 (x = 0.00, 0.03, 0.04, 0.05) by means of a combination of Mössbauer spectroscopy, XPS, HRTEM, dielectric and anelastic spectroscopy. We found that Fe ions are substituted as Fe3+ at Ti sites and preferentially exhibit pentahedral coordination, whereas Ti ions have coexisting valences of Ti4+/Ti3+. Fe3+ ions are preferentially ordered in clusters, and there exists a transition temperature TC1, below which phase separation occurs between a tetragonal phase T1 free of magnetic clusters and a cubic phase, and a lower transition temperature TC2, below which the cubic phase rich in magnetic clusters is transformed into a tetragonal phase T2. The phase separation persists at the nanoscale level down to room temperature and is visible in HRTEM images as a mixing of nanodomains with different tetragonality ratios. This phase separation was observed over the whole studied concentration range of xFe values. It occurs progressively with the value of xFe, and the transition temperature TC2 decreases with the concentration from about 620 K (xFe = 0.03) to about 600 K (xFe = 0.05), while TC1 remains nearly constant.