Housing and transport affordability (H + TA) analysis has been receiving increasing attention among academics and practitioners worldwide, particularly in Global North settings. These studies usually overlook spatial and socioeconomic distributional considerations that potentially underestimate the simultaneous impact of transport and housing costs on lower-income family budgets. Our work seeks to address these knowledge gaps by understanding and measuring H + TA, considering different types of households in Santiago, Chile. Combining income, housing, transport, and census data, we estimate H + TA costs using spatial clusters and probability distribution functions, analyzing the “degree of choice” that socially disadvantaged groups have given their financial constraints. The results show that families with children, the elderly, and immigrants are among the most limited in their choices. Most central and eastern sectors of the city which provide the highest density of work opportunities are out of reach for the three lowest-income deciles given the high combined costs of H + TA, being dependents on government benefits and/or social housing. Middle class, from the 4th to 6th income deciles, can choose from between 30% and 65% of all housing and transport combinations, but from less than 6% of those offered on the two clusters with the best transport and urban conditions. These findings bring into question current inter-sectoral policies to alleviate the “cost pressure” of Santiago’s lower- and middle-income households.