;6 July 2016 — Limoges to Le Lioran, This medium mountain stage departed east from Limoges, over the Category 4 Côte de Saint-Léonard-de-Noblat, through Bujaleuf and turning south-east to Eymoutiers. The riders continued through Bugeat and Meymac to Saint-Angel. The race then turned south to head through Neuvic before climbing the Category 3 Côte du Puy Saint-Mary, quickly followed by an intermediate sprint through Mauriac. The riders continued south-east through Anglards-de-Salers and Salers ascending the Category 3 Col de Neronne to. A brief descent was followed by the Category 2 climb of the Pas de Peyrol to. The race then descended south on a winding route through Mandailles to the Category 2 climb of the Col du Perthus to. Following this climb, the riders descended through Saint-Jacques-des-Blats, and turned north-east to climb the Category 3 Col de Font-de-Cère to, before a brief descent and climb to the finish line at Le Lioran.
;7 July 2016 — Arpajon-sur-Cère to Montauban, This hilly to flat stage departed south from Arpajon-sur-Cère, through Montsalvy to Vieillevie. The riders then headed west through Saint-Parthem to the Category 3 climb of the Col des Estaques to. The descent south into Decazeville was followed by the Category 4 climb of the Côte d'Aubin to. This then gently ascended into the intermediate sprint at Montbazens, where the route turned south-west. The race then travelled through Lanuéjouls, Villefranche-de-Rouergue, Parisot and Saint-Antonin-Noble-Val where the riders turned west to climb the Category 3 Côte de Saint-Antonin-Noble-Val to. Following the descent south-west into Montricoux, the race continued through Saint-Étienne-de-Tulmont to a flat finish at Montauban.
Stage 6 result
Stage 7
;8 July 2016 — L'Isle-Jourdain to Lac de Payolle, This medium mountain stage departed from L'Isle-Jourdain, heading south-west through Lombez to Boulogne-sur-Gesse. The race then turned west travelling through Castelnau-Magnoac and Trie-sur-Baïse to Chelle-Debat. The route then turned south through Bordes and south-east to ascend the Category 4 Côte de Capvern, continuing without descent into La Barthe-de-Neste. The riders then headed south through an intermediate sprint at Sarrancolin, continuing to Arreau before turning west to begin the climb of the Category 1 Col d'Aspin to. The riders then had a descent to the finish line at Lac de Payolle. Steve Cummings won the stage with a solo attack. After the first five riders passed, the red inflatable marker collapsed, blocking chasing riders, so the race organisation decided to use the timegaps measured at the mark. Adam Yates was most affected by the collapsing flamme rouge, because he was 7 seconds in front of the other favorites at that moment, and the marker collapsed right in front of him, causing him to crash into it. After the podium ceremony the commissaires revised the result, moving Yates into second place on the General Classification and into the white jersey, which he wore non-stop for the remainder of the 2016 competition.
Stage 7 result
Stage 8
;9 July 2016 — Pau to Bagnères-de-Luchon, This mountainous stage departed from Pau, heading south-east, through Lestelle-Bétharram, to Lourdes. The race then turned south through Ayros-Arbouix and Villelongue, with an intermediate sprint at Esquièze-Sère, just before Luz-Saint-Sauveur. The route then headed east through Barèges to traverse the Hors catégorieCol du Tourmalet, a climb to for the Souvenir Jacques Goddet, with a descent into Sainte-Marie-de-Campan. The race then turned south and began the immediate ascent of the Category 2 La Hourquette d'Ancizan to and descended into Saint-Lary-Soulan. The riders then turned east, once again, and ascended the Category 1 Col de Val Louron-Azet to, descending into Loudenvielle. The final climb was the Category 1 Col de Peyresourde at, before descending to the finish line at Bagnères-de-Luchon. Michael Mørkøv, who had been battling with injuries all week, became the first rider to withdraw from the tour. This set a new all-time record for the longest time in which the peloton had remained intact prior to the first withdrawal. Chris Froome won the stage after surprisingly breaking away from a group of 14 riders just before the summit of the Col de Peyresourde, with about 15 km remaining. On the descent into Bagnères-de-Luchon he adopted a 'super aero' position, pedalling as he did so reaching a top speed of 90.9 km/h. With 10 km to go Froome opened up a gap of 11 seconds and he maintained the lead to the end, with the following pack finishing 13 seconds behind. With the time bonus, Froome took the yellow jersey for the first time in the race, wearing it non-stop through the remainder of the 2016 competition.
Stage 8 result
Stage 9
;10 July 2016 — VielhaVal d'Aran to Andorre Arcalis, This mountainous stage departed from Vielha Val d'Aran in Spain, heading east over the Category 1 climb of the Port de la Bonaigua to. The riders then headed south-east through La Guingueta d'Àneu, and turned south-west at Llavorsí, to the valley floor at Sort. The route then turned south-east for the climb of the Category 1 Port del Cantó to, descending to the valley floor at Montferrer i Castellbò. From La Seu d'Urgell, the race climbed north to an intermediate sprint at Andorra la Vella, and continued climbing into the Category 2 summit of the Côte de la Comella at. Following a short descent to Encamp was the Category 1 climb of the Col de Beixalis to. The race then descended to Ordino, before beginning the Hors catégorie climb to for the finish line at Andorra Arcalis. Two time overall winner Alberto Contador, one of the pre-race favorites, abandoned the Tour during Stage 9.
;12 July 2016 — Escaldes-Engordany to Revel, In this medium mountain stage, the riders departed from Escaldes-Engordany in Andorra, heading east over the Category 1 climb of the Port d'Envalira to. The riders then descended north-east back into France to Ax-les-Thermes, and turned north-west still gradually descending towards Tarascon-sur-Ariège. The race then turned north-east towards Mercus-Garrabet and wound east through Nalzen to Lavelanet. The route continued north-east to an intermediate sprint at Aigues-Vives. The riders then continued north through Mirepoix, Plavilla, Fendeille and Castelnaudary reaching the short Category 3 climb of the Côte de Saint-Ferréol. The race then descended to the finish line in Revel. Peter Sagan took the green jersey for the third time in the 2016 competition, and wore it non-stop for the remainder of the Tour.
Stage 10 result
Stage 11
;13 July 2016 — Carcassonne to Montpellier, This flat stage departed from Carcassonne, heading east through Caunes-Minervois and Siran to the Category 4 climb of the Côte de Minerve to. The riders then descended to Aigues-Vives, and turned north-east to climb the Category 4 Côte de Villespassans to descending through Saint-Chinian to Cessenon-sur-Orb. Continuing east, the riders passed through Murviel-lès-Béziers, Magalas and Alignan-du-Vent to an intermediate sprint at Pézenas. The race then headed through Montagnac, passing Valmagne Abbey, and continuing on through Montbazin. Bearing towards the north-east, the race headed through Pignan to the finish line in Montpellier.
