The 27-year-old Spaniard out-paced fellow attacker David de la Cruz (Quick-Step Floors) on the steep final climb of Picón Blanco to extend his overall race lead, having already won the opening stage.
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Enric Mas (Quick-Step Floors) came in for third place at 41 seconds.
Landa now leads de la Cruz by 27 seconds overall, with Mas in third at 46 seconds.
Ten riders formed a break just after the start in Ojo Guareña: Dorian Godon (Cofidis), Bernardo Suaza (Manzana Postobon), Lasse Norman Hansen (Acqua Blue Sport), Fabien Grellier (Direct Energie), Janse Van Rensburg (Dimension Data), Fabricio Ferrari (Caja Rural), Gatis Smukulis (Delko Marseille Provence KTM), Jorge Cubero (Burgos), Martijn Budding (Roompot Nederlandse Loterij) and Pieter Serry (Quick-Step Floors).
Over the day’s almost relentless selection of classified climbs and rolling terrain, the break was enduring a tough day. Smukulis was evidently the strongest, and went solo after the Alto de Ailanes opening up a gap on his former companions.
Smukulis had just over two minutes ahead of the Sky-led peloton as he hit 10km to go. However, he had his work cut out for him facing the final climb of 8.5km at an average of 9.1 per cent, but with sections of over 11 per cent.
By the foot of the climb two kilometres later, Smukulis was fading, and the gap was down to under a minute. He was caught with 6.3km to go, and swung over at the side of the road at a virtual standstill as the peloton passed him.
Sky continued to set the speed of the bunch, but it proved to be too much for the majority. With 4km to go, there were just four riders accompanying Sky’s Gianni Moscon and Landa. Quick-Step also had two riders: Mas and de la Cruz, plus Jaime Rosón (Caja Rural) and Miguel Angel Lopez (Astana).
Mas attacked inside 4km, forcing Moscon to waste energy in trying to chase. All the while, Landa sat on his team-mate’s wheel, biding his time.
Moscon swung off with 3.2km to go, leaving Landa to quickly chase down Mas and drag the others up to him. De la Cruz attacked almost immediately when the catch was made, followed by Landa – leaving Rosón, Lopez and Mas behind.
Landa and de la Cruz continued riding ahead of the three chasers and it became obvious that the stage win was going to be contested between the two riders. However, there was to be no gift to de la Cruz, as Landa accelerated away from him in the final 500 metres to take his second stage win of the race.
The 2017 Vuelta a Burgos continues on Friday with the race’s flattest stage, a 147-kilometre trip from Bodegas Nabal to Clunia. The day may not be one for the sprinters, though, as there is a short, steep kick up to the line. The UCI 2.HC-ranked race concludes on Saturday, August 5.
Vuelta a Burgos 2017, stage three: Ojo Guareña to Picón Blanco, 173km
1. Mikel Landa (Esp) Team Sky, in 4-36-40
2. David de la Cruz (Esp) Quick-Step Floors, at 9 secs
3. Enric Mas (Esp) Quick-Step Floors, at 41 secs
4. Jaime Rosón (Esp) Caja Rural-Seguros RGA, at 47 secs
5. Miguel Ángel López (Col) Astana, at 55 secs
6. Igor Anton (Esp) Dimension Data, at 1-06
7. Merhawi Kudus (Eri) Dimension Data, at 1-24
8. Gianni Moscon (Ita) Team Sky, at 1-27
9. Jetse Bol (Ned) Manzana Postobon, at 1-33
10. Sergio Pardilla (Esp) Caja Rural-Seguros RGA, at 1-34
General classification after stage three
1. Mikel Landa (Esp) Team Sky, in 11-41-32
2. David de la Cruz (Esp) Quick-Step Floors, at 27 secs
3. Enric Mas (Esp) Quick-Step Floors, at 46 secs
4. Jaime Rosón (Esp) Caja Rural-Seguros RGA, at 54 secs
5. Miguel Ángel López (Col) Astana, at 1-02
6. Igor Anton (Esp) Dimension Data, at 1-13
7. Merhawi Kudus (Eri) Dimension Data, at 1-31
8. Gianni Moscon (Ita) Team Sky, at 1-34
9. Jetse Bol (Ned) Manzana Postobon, at 1-40
10. Sergey Chernetskiy (Rus) Astana, at 1-42