We have little documentation covering the period up to the ninth century. The chronicle of Alfonso III, c. 880, reports that the king's predecessor, Alfonso I, resettled Carranza and Sopuerta. The first written document mentioning the valley of Somorrostro—of which Muskiz is just one part—dates from 1068. Roman culture does not seem to have changed the habits and customs of the local population, who continued to exploit the arable and livestock resources of badly defined territorially domains.

The period between the 9th and 14th centuries was one of major change, with the assimilation of Christianity; the appearance of the tower-house as a centre of power replacing even the church; economic diversification (iron and trade); the appropriation of common lands; the breakdown of traditional society; an increase in social inequalities between different sections of the population and restructuring of settlement patterns with the emergence of new institutions— the town (or villa), the worker's district (barriada) and the farmstead (caserío).
As Christianity spread, a new economic and social feature began to emerge: the church. Churches became more widespread from the 11th century on. Among the oldest in the area are the church of Santa María in Pobeña and the church if Cerrada de Ranes, in Cardeo.

These buildings were small and architecturally simple. In the neighbouring land there was a burial ground for members of the community. Although the funerary rite itself was Christian, pre-Christian rituals of protection and worship of the dead endured. The church was also a major economic centre, creaming off the scarce agricultural surplus through the tithe system. Churches were privately owned, and like any other asset could be sold, donated, etc. Their owners enjoyed certain rights over other local people. Saint María in Pobeña was owned by Doña Elo Bellacoz and had grazing lands, orchards and a harbour, which suggests some maritime activity. In the thirteenth century, the Lord of Biscay, Diego López de Haro (nicknamed the Good) presented various churches in the valley of Somorrostro, including San Julián, to Sancho Ortiz Marroquín de Montehermoso for his services at the battle of Navas de Tolosa.

In the fourteenth century, a period of economic crisis set in; the nobles strove to prevent a fall in their income and disputes arose among them as to who was “worth more”, in other words, who had more income, wealth and profit. We can learn much about late Medieval Biscay from Lope Garcia de Salazar's account “Bienandanzas e Fortunas”, which chronicles some of these inter-faction conflicts. The Salazar family, to which the chronicler belonged, ruled over the valley of Somorrostro from its castle at Muñatones. This Salazars settled in Muskiz around 1256 when they married into the Muñatones family. Like other more important relatives, the family possessed lands, earth and men, enjoyed an income and exemption from taxation and subjected the inhabitants of the area to its authority.

During this period, a large number of tower houses were built at strategic sites (roads, ports, etc.), nearly always close to chapels, forges and mills, evidencing the great social instability of the time. The arrival of the Salazars in Muñatones led to a proliferation of towers in Muskiz. Controlling the territory from their main castle the family installed their kinsfolk in different districts of the town: Pobeña, Montaño, Memerea, San Julián, Santelices, La Rigada. These tower houses became centres for exploiting and administering local resources. The most significant building of the period was Muñatones Castle.