This study analyzes the productive structure of Portugal in the period 2013–2017, using indicators of localization and specialization applied to 308 Portuguese local authorities. From an empirical approach using a threshold model, the following indicators are used: (i) localization quotient; (ii) specialization coefficient; (iii) Theil entropy index; (iv) rate of industrialization; and (v) the density of establishments by business size. The selected period 2013–2017 is due to the available data concerning firms located per local authority, and the choice of threshold model is justified through the possibility of assessing the non-linear effects of specialization and diversification on productivity, considering, in simultaneous terms, different regimes per business size. Estimation of the threshold model identified a positive, statistically significant relation between industrialization and productivity. Similarly, the terms of interaction between exports and diversification, and between the former and higher education institutions, shows a catalyzing effect of productivity. In addition, the most specialized micro-firms affect productivity significantly and positively, while the least specialized have the opposite effect. Small, less specialized companies have a significant and negative effect on productivity, contrasting with less specialized, medium-sized companies, which affect productivity positively. For large firms, the impact on productivity is negative for both high and low levels of specialization, reinforcing the need to fill existing gaps in strategic diversification, as well as the vertical and horizontal integration of the activities of production chains with high value added.