The use of caves and/or rock shelters as a refugee for herds was a common practice in the Mediterranean area since the early Neolithic. Shepherds move the herds to pastures in higher altitudes, away from the settlements where the animals graze nearby the shelters where livestock is regrouped. Dung and residues produced during the occupation of these shelters were generally heaped and burnt to clean the site and prepare it for new usage, forming a characteristic deposit known as fumier. Fumier deposits are a great source of information to understand past herding practices including the animal's stabled, the management of the residues, the landscape, and the use of plants. In addition, they can provide a better understanding of site formation and postdepositional processes of archaeological sediments in caves and shelters including the impact of fire. Specific microarchaeological analyses are usually utilized to study fumier deposits. Here we present a multi-proxy approach that includes phytoliths, spherulites, ash pseudomorphs, and FTIR analyses, applied to the Neolithic levels of San Cristóbal, Los Husos II (Álava, Spain) and El Mirador (Burgos, Spain), located in the upper Ebro and Duero basins. This area in the north of the Iberian Peninsula constitutes a strategic location for the spread of the productive economy to the north, west, and interior of the Iberian Peninsula. Except for the lower Level XIII of San Cristóbal, where domestic activities were documented, our results showed similar behavior for the three studied sites, with no significant differences neither in terms of plant presence nor in the formation processes of the deposits. Up to seven and two possible complete stabling episodes were identified: three and two possible ones in San Cristóbal, and four in Los Husos II. Among the plants identified grasses of the C3 Pooideae subfamily were dominant, probably representing local grasses. The combining presence of thermally altered phytoliths, spherulites, and ash pseudomorphs points that the stabling episodes burned for several hours with temperatures ranging between 500 °C and 700 °C.